MacFixIt reader Steve Summers found a culprit cache file that was causing fonts to not auto-activate through Extensis' Suitcase:
"I tried the normal tricks; making sure the correct options were set in Suitcase and in the Auto-Activation plug-in for Illustrator, replacing my Illustrator preferences with backups I keep, deleting the Suitcase preferences and re-dropping my fonts into Suitcase. I got more desperate as nothing seemed to help. I moved on to deleting any instance of an AdobeFnt.lst file, and any user-level font-related cache or database file. None of this worked as it usually did. I finally decided to dive deeper into the system.
"I logged out and back in as 'root.' In my search for various caches which might be the culprit, I ran across a file in the System/Library/Caches/ directory which was named 'fontTablesAnnex.' It's size was a suspicious 10.8MB. Not knowing what exactly was kept inside, but pretty sure it would be rebuilt, I dragged it to the trash, but didn't delete it (just in case).
"I restarted, logged in as a normal user, and started up Suitcase and Illustrator as I normally would. I then opened the document I had been having problems with, and the fonts were auto-activating again [...] I'm guessing that this file hadn't been purged and refreshed in a while, because the new file it created was much smaller; less than 200KB."
So if you are having problems with fonts auto-activating through Suitcase, search out this file and put it in the Trash or another place where you can retrieve it later, restart, and check for auto-activation.
Instead of logging in as the root user, as suggested by Summers, you can use an invisible file tool like Invisible Finder to seek out the fontTablesAnnex file.