Gee, I still don't use Acrobat X very much, and I'm not sure I've ever opened a Visio PDF; plus when Acrobat 9 reports images have been replaced I'm usually the one who did the replacing and don't need Acrobat to tell me. So I'm not sure I can say anything very helpful.
One error I frequently make is failing to set the "Document Description" for the comparison: I almost always want Reports, etc. (i.e., a text comparison), but my Acrobat 9 defaults to Scanned Documents, which I rarely want but which might help here. I also forget to limit the range of pages, as described in last year's post.
I assume you've been getting the kind of comparison you want, but it may be worth exploring Acrobat's options for displaying the comparison: would displaying old and new side by side give you what you need? I have worked with a sided-by-side comparison open, and toggled Acrobat to a copy of the new version to add Acrobat commenting mark-ups there.
Even without side-by-side display the comparison can show both old and new images. These can be distorted for comparison's other than with the Scanned documents setting if the image's pixel dimensions change, but for a diagram the way that setting displays the comparison image might be useful. If not, and because I work mostly in InDesign, I might be tempted to create a new ID file, with the two PDFs on separate layers, allowing me to toggle the layers' visibility in ID to help me find differences -- the modern equivalent of the old typesetter's trick of putting old and new printouts on the light table to highlight differences. I would not be surprised if one could use Acrobat layers similarly, and of course Photoshop can do this for single PDF pages.
Good luck,
David