Hi again Tim,
Yes, when I turned those problematic fonts off I saw those messages about some of them being system fonts. However, they were mostly foreign language fonts (that I figured I didn't use anyway). Actually, the fonts that are really necessary to the system can't be turn off in Font Book (see link below) so there's really not much to worry about.
http://support.apple.com/kb/HT1538
Anyway, other than turning them off, I don't know of any other solution. Hopefully someone else will come along who does; I'd like to know the answer myself :-)
