In a prepress environment, FontBook doesn't cut the mustard. It works well if you don't use a ton of fonts and you don't need to activate or deactivate often.
We use Suitcase 11.0.4 with Font Doctor. For problems I use several methods.
1. Do a find and look for adobefnt files. Delete all adobefnt files (just the .lst files, not the .db files).
2. In the Quark application folder is a sub folder named Jaws. Open that up and delete the "ttfont" folder. (It will regenerate upon quark restarting).
3. Download and use
fontfinagler to keep your mac clean.
4. Keep your system fonts to a minimum. Check out
this thread on the Apple web site.
Hope this helps,
David