There may be a problem with file permissions. To change all FontAgent Pro's fonts permissions:

1. Download BatChmod from http://www.macchampion.com/arbysoft/batchmod_137.dmg and launch it
2. Click File and select the FontAgent Pro Fonts folder
3. Change Owner permissions to root (RWX)
4. Change Group permissions to Admin (RWX) Everyone (RX)
5. Check "Apply ownership and privileges"
6. Click Apply