In addition to the problems with cross-reference markers, it seems that Variables are affected as well. I use WebWorks ePublisher Pro 9.2 build 10315 to convert my FM8 documents to CHM or other formats. After applying this patch, the variables now appear blank in ePublisher Pro and in the output.
I tried uninstalling the patch and that did not work. I saved my document as FM7.2 and ran it through ePublisher Pro again, and it worked, the Variables were populated.
I have put in a support request to Adobe and will share their response with the forum.