Linotype's Font Explorer X will delete System Font Caches and Application Font Caches (unsure if it handles FMP's cache).
Applejack removes system caches
Info about Applejack
Onyx will also deal with caches
As will many other utilities, including Tiger Cache Cleaner, Leopard Cache Cleaner, and others.
One of the easy ways to narrow the possible problems, is to go to System Preferences > Users > click the lock icon, authenticate, create new user TEST, close system preferences.
Logout as currentuser, login as TEST and test FMP.
If the symptoms are gone, the problem most likely lies with a corrupt preference file (plist), a corrupt font that is not installed for this user, or a corrupt cache (likely a font cache).