Acrobat XI Pro, View | Compare Document functionality

I've been using the document compare functionality in Acrobat Pro for years, but I only recently switched from Adobe Acrobat 9 Pro to Adobe Acrobat XI Pro. The documents I compare are admittedly quite complex. However, when I run the document compare feature in Acrobat XI Pro using any combination of document descriptions, almost everything on the page is marked with the color of 'replace color' on both documents, so virtually every line and every word is marked. The issue is that about 95% items that are marked with the 'replace color' are identical between the two documents. As a result, since everything is marked as 'different', it is now almost impossible to find actual differences between the two documents--I may as well print them out and proof read the documents manually. I've tried almost every setting I can think of to solve this problem to no avail. Is there a way to get the Compare Document functionality to work correctly in Adobe Acrobat XI Pro? Is there a work around, or is the Compare Document functionality just broken in Acrobat XI Pro?