Thank you, Shashikant. I had to split this into two posts because of the character limit. 

I've tried to condense the code to its essentials. The problems area denoted by ' ==> ' in the left margin.


==> The apex code below is part of a larger class. The two variables that I don't understand the behavior are application.Shipping_Country__c & application.Billing_Country__c. Basically, when these variables are used in the first pageReference, "/apex/MembershipApplication" the page uses the user selected, new items. This is expected. However when the other pageReference is called, '/apex/MembershipApplicationPDF' , the page uses the old variables used before the user edited. This is despite the fact that the debug log that I call at the beginning of the makePDF method shows the correct value in the Shipping_Country__c & Billing_Country__c. Additionally, the other address fields are work as expected. 


public PageReference customSave()
    {
        System.debug('starting custom save');
        Boolean isError = false;
       
        // do validations first   
       
        // since so many validations depend on the domains, do them first and return if a problem
        Boolean isDomainError = false;
        isDomainError = isDomainValidated( application.Approved_Company_Domains__c, application.Website__c );
        if ( isDomainError )
        {
            return null;
        }
       
        isError = isValidated( memberList, application.Approved_Company_Domains__c );
        System.debug('after validations: isError: ' + isError);
                 
        // have we encountered any problems to address before saving?
        if ( isError )
        {
            // if yes, return to the page and display the error message
            System.debug( 'did not pass validations...');
            return null;
        }
       
        try
        {
            // expire the applicaton to prevent re-edits...
            application.Application_Expiration_Date__c = Date.Today() - 1;
           
            if ( newContactList != null && newContactList.size() > 0 )
            {
                    system.debug('inserting new contacts: ' + newContactList);
                    upsert newContactList;
            }
            if ( existingContactList != null && existingContactList.size() > 0 )
            {
                    system.debug('updating existing contacts: ' + existingContactList);            
                    upsert existingContactList;
            }
            if ( inactiveContactIdList != null && inactiveContactIdList.size() > 0 )
            {
                userList = getUsersForDeactivation( inactiveContactIdList );
                if ( userList != null && userList.size() > 0 )
                {
                    for ( User u : userList )
                    {
                        u.Portal_Access__c = 'Inactive';
                        u.IsActive = false;    
                    }
                    system.debug('updating users: ' + userList );
                    update userList;
                }                      
            }
           
            // if no problem, save the application
            system.debug( 'updating application: ' + application );
   application.Submitted__c = true; 
            update application;

            system.debug('shipping address country: ' + application.Shipping_Country__c);
            system.debug('billing  address country: ' + application.Billing_Country__c );
           
        }
        catch(Exception e)
        {
            System.debug('caught exception saving MMA Application: ' + e.getMessage() );
            MessageHelper.addError( 'Encountered a problem saving the Membership Application.  The error was: ' + e.getMessage() );
            return null;                   
        }
      
       
        PageReference pageRef = new PageReference('/apex/MembershipApplication');
        pageRef.setRedirect( false );
        System.debug( 'setting redirect to: ' + pageRef.getUrl() ); 
        MessageHelper.addStatus( 'Application Submitted');
       
        // set the submitted flag to "true" to show the confirmation message; make it "expired" to make fields read-only when viewing confirmation
        isSubmitted = true;
        isExpired = true;
       
        // let's remove any empty members from the list that were never used so we don't see empty rows in the Contacts on the confirmation screen
        List<MemberWrapper> tmpMembers = new List<MemberWrapper>();
         tmpMembers.addAll( memberList); // make a copy so we're not changing the list while looping...
        Integer i = 0;
        if ( tmpMembers != null && tmpMembers.size() > 0 )
        {
            System.debug( 'memberList size: ' + memberList.size() );
            for ( MemberWrapper wrapper : tmpMembers )
            {
                System.debug( 'tmpMembers size, position: ' + tmpMembers.size() + ' ,' + i);   
                        System.debug('looking for blanks: ' + wrapper.contact.firstname + ' ' + wrapper.contact.lastname );
               
                if ( wrapper.contact == null || (MessageHelper.isBlank( wrapper.contact.firstName) && MessageHelper.isBlank( wrapper.contact.lastName) ))
                {
                        selectedChildIndex = wrapper.index;
                        system.debug( 'removing blank wrapper at position: ' + wrapper.index + ' ' + wrapper );
                        removeChild();
                }      
                i++;
            }
        }      
       
        application.Shipping_Country__c = shippingCountryName;
        application.Billing_Country__c  = billingCountryName;       
       
  makePDF();
           
        // Once everything is verified and written create a PDF version of the MAP and store it in Membership Documents related list.
        //update application;
        return pageRef;
       
    } // end customSave
   
   
    public void makePDF() {
==> Here, I log the variables' values. They are the value we want. But when the PDF is generated it uses a previous value. I included the snippet of VisualForce code that uses this variable at the end of this post.
        System.debug('--> Start makePDF()');
        System.debug('Shipping_Country__c before PDF: "' + application.Shipping_Country__c +'"');
        System.debug('Billing_Country__c  before PDF: "' + application.Billing_Country__c +'"');
        System.debug('Shipping_Country_PDF__c before PDF: "' + application.Shipping_Country_PDF__c +'"');
        System.debug('Billing_Country_PDF__c before PDF: "' + application.Billing_Country_PDF__c +'"');
       
        PageReference pdf = new PageReference('/apex/MembershipApplicationPDF');
        Blob body;
       
        try {
            System.debug('Performing try pdf.getContentAsPdf()');
            body = pdf.getContentAsPdf();
        } catch (VisualforceException e) {
            System.debug('PDF Generation Error: ' + e);
            body = Blob.valueOf('Error : ' + e);
        }
        Id memDocId = null;
        for(Account accIt : [SELECT Id, Name, (Select Id, OwnerId, Name, Membership_Document__c, Document_Type__c From Membership_Documents__r) FROM Account WHERE Id=:AccountId]){
            for(Membership_Document__c md : accIt.Membership_Documents__r) {
                if (md.Document_Type__c == 'Membership Agreement') {  // If the related list already contains a Membership Agreement container then assign that.
                    memDocId = md.Id;
                }
                System.debug('--> MemDocs: ' + md);
            }
            if (memDocId == null) {  // If above related list had no container then create one in that related list.
                Membership_Document__c newMemDoc = new Membership_Document__c();   
                newMemDoc.Document_Type__c = 'Membership Agreement';
                newMemDoc.Name = 'Membership Agreement';
               
                newMemDoc.Membership_Document__c = accountId;
                insert newMemDoc;
                memDocId = newMemDoc.Id;
            }
           
            // insert the PDF attachment into the container that was created or found above.
            Attachment attach = new Attachment();
            attach.Body = body; 
            attach.Name = 'MAP - ' + application.Account_Name__c + ' ' + Datetime.now().format('yyyy-MM-dd HH:mm') + '.pdf';
            attach.isPrivate = false;
            attach.ParentId = memDocId;
            insert attach;
           
        }
        System.debug('--> End makePDF');
    }