Hm. The "All Fonts" collection in Font Book should display every font you have on your computer by name.
The System/Library/Fonts folder is owned by the computer and should not be altered: http://support.apple.com/kb/HT2435
If you have fonts installed in /Library/Fonts and /System/Library/Fonts, they should appear in Font book. If you are running any non-Apple Font managers like Extensis Suitcase, turn them off: http://www.extensis.com.
If installing the update does not help then I would suggest you backup your data and reinstall the OS: http://docs.info.apple.com/article.html?path=Mac/10.6/en/8177.html
Best of luck to you.