Fonts disabled in Font Book all still on in applications (after SL upgrade)

I've successfully upgraded to Snow Leopard on my 2Ghz intel mac. I had some initial problems with fonts but all now working except that despite fonts being disabled in Font Book they are still active in all applications. As I have 500+ this is really annoying.
I've run Disk Utility. What else? - any ideas how to sort this out???

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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