Loaded fonts not available to apps

Running 10.6.8, using Font Agent Pro, have not had problem for past year and a half, and all of a sudden yesterday, fonts not recognized by apps. Using Quark, versions 6 - 9, Adobe Creative Suites CS3 - CS6, Word, Excel, etc. I have loaded fonts through Fontbook instead of using Font Agent Pro, I have removed caches with terminal, ran Repair Disk Permissions, Shutdown, boot in Safe Mode, everything I can think of. In Fontbook, fonts display correctly but a lot of them are not available in other Apps. For instance, Arial & Arial Bold not available, but Italic & Bold Italic are fine. I work at a commercial printer and this is killing me!

Did you repair permissions and restarted your computer after the font installatons?

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