Could you try booting from the installer CD and running Disk Utility from there, By inserting the disk and boting with the C key held down.you may have to Verify and Repair more than once before the errors stop.
Thencould you could also try booting into 9 and running First Aid. Again, you may have to run the Verify and Repair more than once.
Let us know how you get on.
The BSD errors are being caused by switching between your classic environment and your OSX environment.
I am unaware of any method to stop this from happening other than upgrading your OSX to a newer version that uses a a diferent BSD core.
Let me check with another mac expert here and see if he has any input.
OS X.3 and abovehas has Classic support built in http://kb.iu.edu/data/ajel.html so that you can run your older applications without the trouble you are experiencing.
To be honest OSX and 9 dont play well together so you will continue to get the BSD errors,However you can repair them using the methods you already know and you should experience no problems or issues other thanthe occasional BSD message.
I appreciate the accept and the generous bonus.
Thanks for the other links also, I was aware of Rosetta but I thought you had 10.3 so I thought you might wish to check out classic as it is very stable and allows a lot more functionality for older applications.