Disabled fonts still active in applications!

For some strange reason, fonts that I have disabled in Font Book are still showing up in active applications. This started happening after I moved my Users directory off of the startup drive to another internal drive.
Why is this happening and what can I do?

The database for Font Book is in a completely different location in Snow Leopard. The update doesn't seem to always do the hand off correctly as I've seen a fair number of posts stating the same problem. Resetting Font Book's database should fix it.
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 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. Any font sets you have created will be gone. Also, all fonts in the three main Fonts folders (System, Library, your user account) will now be active, regardless of their state beforehand.

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