This is related to how the axis client being used interprets the httpProxy settings.  My understanding is that this is being addressed soon.  However, as a workaround, you can alter the CommonsHTTPSender clas delivered with the distribution.  Here is an example:

Code:

/*
 * The Apache Software License, Version 1.1 Copyright (c) 2001-2003 The Apache Software Foundation. All rights reserved.
 * Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
 * following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of
 * conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice,
 * this list of conditions and the following disclaimer in the documentation and/or other materials provided with the
 * distribution. 3. The end-user documentation included with the redistribution, if any, must include the following
 * acknowledgment: "This product includes software developed by the Apache Software Foundation
 * (http://www.apache.org/)." Alternately, this acknowledgment may appear in the software itself, if and wherever such
 * third-party acknowledgments normally appear. 4. The names "Axis" and "Apache Software Foundation" must not be used to
 * endorse or promote products derived from this software without prior written permission. For written permission,
 * please contact apache@apache.org. 5. Products derived from this software may not be called "Apache", nor may "Apache"
 * appear in their name, without prior written permission of the Apache Software Foundation. THIS SOFTWARE IS PROVIDED
 * ``AS IS'' AND ANY EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
 * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE APACHE SOFTWARE FOUNDATION
 * OR ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
 * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE. ==================================================================== This software
 * consists of voluntary contributions made by many individuals on behalf of the Apache Software Foundation. For more
 * information on the Apache Software Foundation, please see <http://www.apache.org/>.
 * ====================================================================
 * ==================================================================== This file is based on the CommonsHTTPSender that
 * ships with Axis 1.1 It has the following changes from that version a) the ConnectionManager is now static, so that we
 * do connection pooling across instances of the class b) we set the hostConfiguration so that proxy settings get picked
 * up correctly. c) the following values are pulled from settings.xml max connections max connections per host
 * connection factory timeout connection timeout [the data timeout continues to be set from the message context] d) the
 * axis specific logging code is pulled
 *
 *  * Copyright (c) 2005, salesforce.com, inc.
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without modification, are permitted provided
 * that the following conditions are met:
 *
 *    Redistributions of source code must retain the above copyright notice, this list of conditions and the
 *    following disclaimer.
 *
 *    Redistributions in binary form must reproduce the above copyright notice, this list of conditions and
 *    the following disclaimer in the documentation and/or other materials provided with the distribution.
 *
 *    Neither the name of salesforce.com, inc. nor the names of its contributors may be used to endorse or
 *    promote products derived from this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
 * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
 * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
 * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
 * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
 * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 */

package com.sforce;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.FilterInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.util.Hashtable;
import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream;

import org.apache.axis.AxisFault;
import org.apache.axis.Message;
import org.apache.axis.MessageContext;
import org.apache.axis.encoding.Base64;
import org.apache.axis.handlers.BasicHandler;
import org.apache.axis.soap.SOAP12Constants;
import org.apache.axis.soap.SOAPConstants;
import org.apache.axis.transport.http.HTTPConstants;
import org.apache.axis.utils.Messages;
import org.apache.commons.httpclient.Credentials;
import org.apache.commons.httpclient.Header;
import org.apache.commons.httpclient.HttpClient;
import org.apache.commons.httpclient.HttpConnectionManager;
import org.apache.commons.httpclient.HttpMethodBase;
import org.apache.commons.httpclient.MultiThreadedHttpConnectionManager;
import org.apache.commons.httpclient.UsernamePasswordCredentials;
import org.apache.commons.httpclient.methods.GetMethod;
import org.apache.commons.httpclient.methods.PostMethod;
import org.apache.log4j.Logger;

import com.sforce.util.TextUtil;


//import shared.util.TextUtil;

/**
 * This class uses Jakarta Commons's HttpClient to call a SOAP server.
 *
 * @author for sfdc Simon Fell (for axis Davanum Srinivas (dims@yahoo.com))
 * @since 136
 */
public class CommonsHTTPSender extends BasicHandler {

    /**
     * SFDC makes use of Axis for a number of different things, we can't configure all the axis clients the same way.
     * You can set the following properties on the message context to control HTTP level features for that particular
     * request. Typically you get these properties into the message context by setting them on the call object (see
     * org.apache.axis.client.Call)
     */
    public static final String JAVA_PROPERTY_PROXY_HOST = "http.proxyHost";
    public static final String JAVA_PROPERTY_PROXY_PORT = "http.proxyPort";
    public static final String JAVA_PROPERTY_PROXY_USERNAME = "http.proxyUsername";
    public static final String JAVA_PROPERTY_PROXY_PASSWORD = "http.proxyPassword";

    public static final String JAVA_PROPERTY_HTTPS_PROXY_HOST = "https.proxyHost";
    public static final String JAVA_PROPERTY_HTTPS_PROXY_PORT = "https.proxyPort";
    public static final String JAVA_PROPERTY_HTTPS_PROXY_USERNAME = "https.proxyUsername";
    public static final String JAVA_PROPERTY_HTTPS_PROXY_PASSWORD = "https.proxyPassword";

    public static final String PROPERTY_PROXY_HOST = "sfdc.proxyHost";
    public static final String PROPERTY_PROXY_PORT = "sfdc.proxyPort";
    public static final String PROPERTY_PROXY_USERNAME = "sfdc.proxyUsername";
    public static final String PROPERTY_PROXY_PASSWORD = "sfdc.proxyPassword";

    public static final String PROPERTY_ACCEPT_GZIP = "sfdc.acceptGzip";
    public static final String PROPERTY_SEND_GZIP = "sfdc.sendGzip";
    private static Logger logger = null;

    static {
        //using the default max connections and host connections
        connectionManager = new MultiThreadedHttpConnectionManager();
    }

    private static HttpConnectionManager connectionManager;

    public CommonsHTTPSender()
    {
        logger = Logger.getLogger(this.getClass());
    }

    /**
     * invoke creates a socket connection, sends the request SOAP message and then reads the response SOAP message back
     * from the SOAP server
     *
     * @param msgContext
     *            the messsage context
     * @throws AxisFault
     */
    public void invoke(MessageContext msgContext) throws AxisFault {
        HttpMethodBase method = null;
        //logger.setLevel(Controller.getConfig().getAxisLoggingLevel());

        try {
            URL targetURL = new URL(msgContext.getStrProp(MessageContext.TRANS_URL));

            // no need to retain these, as the cookies/credentials are
            // stored in the message context across multiple requests.
            // the underlying connection manager, however, is retained
            // so sockets get recycled when possible.
            HttpClient httpClient = new HttpClient(connectionManager);
            httpClient.setConnectionTimeout(5000);
            httpClient.setHttpConnectionFactoryTimeout(5000);

            setHostConfiguration(httpClient, msgContext);

            String webMethod = null;
            boolean posting = true;

            // If we're SOAP 1.2, allow the web method to be set from the
            // MessageContext.
            if (msgContext.getSOAPConstants() == SOAPConstants.SOAP12_CONSTANTS) {
                webMethod = msgContext.getStrProp(SOAP12Constants.PROP_WEBMETHOD);
                if (webMethod != null) {
                    posting = webMethod.equals(HTTPConstants.HEADER_POST);
                }
            }

            Message reqMessage = msgContext.getRequestMessage();
            logger.debug("Request: \n" + reqMessage.getSOAPPartAsString());
            if (posting) {
                method = new PostMethod(targetURL.toString());
                addContextInfo(method, httpClient, msgContext, targetURL);
                ByteArrayOutputStream baos = new ByteArrayOutputStream();
                if (msgContext.containsProperty(PROPERTY_SEND_GZIP)
                && ((Boolean)msgContext.getProperty(PROPERTY_SEND_GZIP)) == Boolean.TRUE) {
                    GZIPOutputStream gzip = new GZIPOutputStream(baos);
                    reqMessage.writeTo(gzip);
                    gzip.finish();
                } else {
                    reqMessage.writeTo(baos);
                }
                ((PostMethod)method).setRequestBody(new ByteArrayInputStream(baos.toByteArray()));
                ((PostMethod)method).setUseExpectHeader(false); // workaround for
            } else {
                method = new GetMethod(targetURL.toString());
                addContextInfo(method, httpClient, msgContext, targetURL);
            }
            int returnCode = httpClient.executeMethod(method);
            String contentType = null;
            String contentLocation = null;

            if (method.getResponseHeader(HTTPConstants.HEADER_CONTENT_TYPE) != null) {
                contentType = method.getResponseHeader(HTTPConstants.HEADER_CONTENT_TYPE).getValue();
            }
            if (method.getResponseHeader(HTTPConstants.HEADER_CONTENT_LOCATION) != null) {
                contentLocation = method.getResponseHeader(HTTPConstants.HEADER_CONTENT_LOCATION).getValue();
            }
            contentType = contentType.trim();
            if ((returnCode > 199) && (returnCode < 300)) {

                // SOAP return is OK - so fall through
            } else if (msgContext.getSOAPConstants() == SOAPConstants.SOAP12_CONSTANTS) {
                // For now, if we're SOAP 1.2, fall through, since the range of
                // valid result codes is much greater
            } else if ((contentType != null) && !contentType.equals("text/html")
                    && ((returnCode > 499) && (returnCode < 600))) {

                // SOAP Fault should be in here - so fall through
            } else {
                String statusMessage = method.getStatusText();
                AxisFault fault = new AxisFault("HTTP", "(" + returnCode + ")" + statusMessage, null, null);

                try {
                    fault.setFaultDetailString(Messages.getMessage("return01", "" + returnCode, method
                            .getResponseBodyAsString()));
                    throw fault;
                } finally {
                    method.releaseConnection(); // release connection back to pool.
                }
            }
            // if we are maintaining session state,
            // handle cookies (if any)
            if (msgContext.getMaintainSession()) {
                Header[] headers = method.getResponseHeaders();
                for (int i = 0; i < headers.length; i++) {
                    if (headers[i].getName().equalsIgnoreCase(HTTPConstants.HEADER_SET_COOKIE))
                        msgContext.setProperty(HTTPConstants.HEADER_COOKIE, cleanupCookie(headers[i].getValue()));
                    else if (headers[i].getName().equalsIgnoreCase(HTTPConstants.HEADER_SET_COOKIE2))
                            msgContext.setProperty(HTTPConstants.HEADER_COOKIE2, cleanupCookie(headers[i].getValue()));
                }
            }

            // wrap the response body stream so that close() also releases the connection back to the pool.
            InputStream responseStream = createConnectionReleasingInputStream(method);
            Header contentEnc = method.getResponseHeader("Content-Encoding");
            if (contentEnc != null && contentEnc.getValue().equalsIgnoreCase("gzip")) {
                responseStream = new GZIPInputStream(responseStream);
            }
            Message outMsg = new Message(responseStream, false, contentType, contentLocation);

            outMsg.setMessageType(Message.RESPONSE);
            msgContext.setResponseMessage(outMsg);

            logger.debug("Response: \n" + msgContext.getResponseMessage().getSOAPPartAsString());
        } catch (Exception e) {
            logger.debug(e);
            throw AxisFault.makeFault(e);
        }
    }

    /**
     * cleanup the cookie value.
     *
     * @param cookie
     *            initial cookie value
     * @return a cleaned up cookie value.
     */
    private String cleanupCookie(String cookie) {
        cookie = cookie.trim();
        // chop after first ; a la Apache SOAP (see HTTPUtils.java there)
        int index = cookie.indexOf(';');

        if (index != -1) {
            cookie = cookie.substring(0, index);
        }
        return cookie;
    }

    private void setHostConfiguration(HttpClient client, MessageContext msgContext) {

        String proxyHost = (String)msgContext.getProperty(PROPERTY_PROXY_HOST);
        Integer proxyPort = (Integer)msgContext.getProperty(PROPERTY_PROXY_PORT);
        String proxyUsername = (String)msgContext.getProperty(PROPERTY_PROXY_USERNAME);
        String proxyPassword = (String)msgContext.getProperty(PROPERTY_PROXY_PASSWORD);

        if(TextUtil.isNullEmptyOrWhitespace(proxyHost)){
            java.util.Properties p = System.getProperties();

            //Retrieve the Proxy Host, if specified
            if(p.containsKey(JAVA_PROPERTY_HTTPS_PROXY_HOST)){
                proxyHost = p.getProperty(JAVA_PROPERTY_HTTPS_PROXY_HOST);
            } else if(p.containsKey(JAVA_PROPERTY_PROXY_HOST)){
                proxyHost = p.getProperty(JAVA_PROPERTY_PROXY_HOST);
            }

            try {
                //Retrieve the Proxy Port, if specified
                if(p.containsKey(JAVA_PROPERTY_HTTPS_PROXY_PORT)){
                    proxyPort = new Integer(p.getProperty(JAVA_PROPERTY_HTTPS_PROXY_PORT));
                } else if(p.containsKey(JAVA_PROPERTY_PROXY_PORT)){
                    proxyPort = new Integer(p.getProperty(JAVA_PROPERTY_PROXY_PORT));
                }
            } catch (NumberFormatException nfe) {
                proxyPort = null;
            }

            //Retrieve the Proxy Username, if specified
            if(p.containsKey(JAVA_PROPERTY_HTTPS_PROXY_USERNAME)){
                proxyUsername = p.getProperty(JAVA_PROPERTY_HTTPS_PROXY_USERNAME);
            } else if(p.containsKey(JAVA_PROPERTY_PROXY_USERNAME)){
                proxyUsername = p.getProperty(JAVA_PROPERTY_PROXY_USERNAME);
            }

            //Retrieve the Proxy Password, if specified
            if(p.containsKey(JAVA_PROPERTY_HTTPS_PROXY_PASSWORD)){
                proxyPassword = p.getProperty(JAVA_PROPERTY_HTTPS_PROXY_PASSWORD);
            } else if(p.containsKey(JAVA_PROPERTY_PROXY_PASSWORD)){
                proxyPassword = p.getProperty(JAVA_PROPERTY_PROXY_PASSWORD);
            }
        }

        if (!TextUtil.isNullEmptyOrWhitespace(proxyHost) && proxyPort != null && proxyPort.intValue() > 0) {
            client.getHostConfiguration().setProxy(proxyHost, proxyPort.intValue());
        }
        if (!TextUtil.isNullEmptyOrWhitespace(proxyUsername) && !TextUtil.isNullEmptyOrWhitespace(proxyPassword)) {
            client.getState().setProxyCredentials(null, null, new UsernamePasswordCredentials(proxyUsername, proxyPassword));
        }
    }

    /**
     * Extracts info from message context.
     *
     * @param method
     *            Post method
     * @param httpClient
     *            The client used for posting
     * @param msgContext
     *            the message context
     * @param tmpURL
     *            the url to post to.
     * @throws Exception
     */
    private void addContextInfo(HttpMethodBase method, HttpClient httpClient, MessageContext msgContext, URL tmpURL)
            throws Exception {

        // optionally set a timeout for the request
        if (msgContext.getTimeout() != 0) {
            httpClient.setTimeout(msgContext.getTimeout());
        }

        if (msgContext.containsProperty(PROPERTY_ACCEPT_GZIP)
                && ((Boolean)msgContext.getProperty(PROPERTY_ACCEPT_GZIP)) == Boolean.TRUE) {
            method.addRequestHeader("Accept-Encoding", "gzip");
        }

        if (msgContext.containsProperty(PROPERTY_SEND_GZIP)
                && ((Boolean)msgContext.getProperty(PROPERTY_SEND_GZIP)) == Boolean.TRUE) {
            method.addRequestHeader("Content-Encoding", "gzip");
        }

        // Get SOAPAction, default to ""
        String action = msgContext.useSOAPAction() — msgContext.getSOAPActionURI() : "";

        if (action == null) {
            action = "";
        }
        Message msg = msgContext.getRequestMessage();
        if (msg != null) {
            method.setRequestHeader(new Header(HTTPConstants.HEADER_CONTENT_TYPE, msg.getContentType(msgContext
                    .getSOAPConstants())));
        }
        method.setRequestHeader(new Header(HTTPConstants.HEADER_SOAP_ACTION, "\"" + action + "\""));
        String userID = msgContext.getUsername();
        String passwd = msgContext.getPassword();

        // if UserID is not part of the context, but is in the URL, use
        // the one in the URL.
        if ((userID == null) && (tmpURL.getUserInfo() != null)) {
            String info = tmpURL.getUserInfo();
            int sep = info.indexOf(':');

            if ((sep >= 0) && (sep + 1 < info.length())) {
                userID = info.substring(0, sep);
                passwd = info.substring(sep + 1);
            } else {
                userID = info;
            }
        }
        if (userID != null) {
            Credentials cred = new UsernamePasswordCredentials(userID, passwd);
            httpClient.getState().setCredentials(null, null, cred);

            // The following 3 lines should NOT be required. But Our SimpleAxisServer fails
            // during all-tests if this is missing.
            StringBuffer tmpBuf = new StringBuffer();
            tmpBuf.append(userID).append(":").append((passwd == null) – "" : passwd);
            method.addRequestHeader(HTTPConstants.HEADER_AUTHORIZATION, "Basic "
                    + Base64.encode(tmpBuf.toString().getBytes()));
        }

        // don't forget the cookies!
        if (msgContext.getMaintainSession()) {
            String cookie = (String)msgContext.getProperty(HTTPConstants.HEADER_COOKIE);
            String cookie2 = (String)msgContext.getProperty(HTTPConstants.HEADER_COOKIE2);

            if (cookie != null) {
                method.addRequestHeader(HTTPConstants.HEADER_COOKIE, cookie);
            }
            if (cookie2 != null) {
                method.addRequestHeader(HTTPConstants.HEADER_COOKIE2, cookie2);
            }
        }

        // process user defined headers for information.
        Hashtable userHeaderTable = (Hashtable)msgContext.getProperty(HTTPConstants.REQUEST_HEADERS);

        if (userHeaderTable != null) {
            for (java.util.Iterator e = userHeaderTable.entrySet().iterator(); e.hasNext();) {
                java.util.Map.Entry me = (java.util.Map.Entry)e.next();
                Object keyObj = me.getKey();

                if (null == keyObj) {
                    continue;
                }
                String key = keyObj.toString().trim();
                String value = me.getValue().toString().trim();

                method.addRequestHeader(key, value);
            }
        }
    }

    private InputStream createConnectionReleasingInputStream(final HttpMethodBase method) throws IOException {
        return new FilterInputStream(method.getResponseBodyAsStream()) {
            public void close() throws IOException {
                try {
                    super.close();
                } finally {
                    method.releaseConnection();
                }
            }
        };
    }
}