I have been tasked with finding some solutions for a problem we are facing with Internet Explorer 11 and Salesforce/Merchantforce.  The problem is that IE11 does not accept how Salesforce is processing AJAX calls to submit data, which generates an error in the console.

Here is the error message:

Unable to get property 'Submit' of undefined or null reference

And the html element that is generating this error:
<select  id="pageId:j_id5:Agreement:j_id9:j_id10:j_id12" name="pageId:j_id5:Agreement:j_id9:j_id10:j_id12" onchange="A4J.AJAX.Submit(&#39;pageId:j_id5&#39;,event,{&#39;similarityGroupingId&#39;:&#39;pageId:j_id5:Agreement:j_id9:j_id10:j_id12:j_id13&#39;,&#39;parameters&#39;:{&#39;pageId:j_id5:Agreement:j_id9:j_id10:j_id12:j_id13&#39;:&#39;pageId:j_id5:Agreement:j_id9:j_id10:j_id12:j_id13&#39;} ,&#39;status&#39;:&#39;pageId:st1&#39;} )"><option value="">--None--</option><option value="Custom CAA">Custom CAA</option>
<option value="Standalone Agreement Document">Standalone Agreement Document</option>
<option value="Standard CAA">Standard CAA</option>
</select>

We are also seeing this same kind of error on some Salesforce pages, like the page describing Inbount/Outbound Change Sets the first time you go to those areas in the Setup sub-site.  The button to dismiss the introduction page are broken and produce similar error messages in IE11.

This is a critical problem as our company is about to roll out IE11 to everyone and these issues are going to impact our end-users who cannot be expected to use non-IE browsers.

We contact Salesforce and they suggested overwriting the meta tag with ApexPages.currentPage().getHeaders().put('X-UA-Compatible', 'IE=9');

The controller for our page is manged and cannot be edited so I have tried adding it in the extension controller and making an new extension controller for just this, but that did not work.

Does anyone have any suggestions?

Thanks in advance.