After troublshooting this for the entire day today the issue seems to be a MIME problem.
If everything is woking perfectly, in Tools > Options > Applications...
You should see 4 or more things related to Adobe like "Adobe Acrobat Forms Document", etc. If you don't see at least 4 MIME entries either your Adobe installation is hosed or your FF installation is hosed. I haven't figured out which is causing the issue.
What I did was remaster my patches from my original Adobe 9.1.0 MSI with the two updates via the command line in the directories with the source files. On the 9.1.0 original file I first remastered my MST transform with the Adobe MST utility. I then applied my patches.
msiexec /a AcroRead.msi /p AdbeRdrUpd912_all_incr.msp
msiexec /a AcroRead.msi /p AdbeRdrUpd913_all_incr.msp
I then uploaded that to my network share, unlinked my group policy, made a new group policy, added a batch file to delete adobe.com from program file and the desktop on system startup even though my MST was supposed to take care of that - it's not a perfect world is it? :-)
I then reapplied my GPO's for both FireFox 3.5.2 and Adobe 9.1.3, I checked to make sure the MIME extensions were there and they were. You might have to go into your Adobe Preferences and select that open in browser setting depending on what happens or adjust your MIME settings in FireFox's options but it should work.
That's what worked for me. It's possible a few other things I did along the way tweaked it out, in my group policy on the first run I did select to upgrade previous group policies, for the remaster and repush I didn't select any previous GPO's to upgrade.
It's hard to tell what one thing tweaked it out or what combination of things tweaked out the install. I did also reinstall Adobe 8.1.5 and FF 3.0.10 before doing all this since our machines currently have that setup, I'm not sure if that affected it either, it's just hard to tell but I don't think it did simply because I had done that several times in troubleshooting this issue.
If anyone else has more specifics that would be great!