If you are in OSX and go into Preferences --> Classic --> Advanced --> 
Rebuild Desktop you can rebuild the classic desktop while in OSX. I have 
found this usually clears weird Classic Bugs.

I have also found that booting into OS9 and running Diskwarrior or 
Norton's causes havoc with OSX because they don't recognise OSX files and 
consider them corrupt. However, if you are not using OSX, and are just 
using 9, DIskwarrior is the best solution IMHO.

Regards,
Nathalie