Symptom: I suddenly noticed that the Carbon apps running in my account only had access to a tiny subset of the fonts installed on my system, whereas Cocoa apps saw all fonts properly. This problem isn't well documented, but I seem to have found one old reference
here.
Solution: I knew this had to be a font cache problem. Font caches are stored in /Library/Caches/com.apple.ATS/ and in that folder are numbered subfolders corresponding to the users on the system (501, 502, 503.. etc.). I then looked in NetInfo Manager at the details for my user to find that my user is number 505. I went to folder 505 and decided to trash all the files therein (because I didn't feel like going through the process of elimination). I logged out, back in, opened a Carbon app and saw my fonts were restored. Success!