Than Font Book most likely needs to be reset. Apps seeing fonts that aren't active (according to Font Book's interface) is a very common symptom of a corrupt FB database. Not the only possible cause, but often.
Restart your Mac and immediately hold down the Shift key when you hear the startup chime to boot into Safe Mode. Keep holding the Shift key until you see a progress bar towards the bottom of the screen. You can let go of the Shift key at that point.
OS X asks you to log in (you will get this screen on a Safe Mode boot even if your Mac is set to automatically log in). Let the Mac finish booting to the desktop and then restart normally. This will clear Font Book's database and the cache files of the user account you logged into in Safe Mode.