Had this EXACT same problem a week ago and it ended up being a bum drive. I had OS 9 on an internal 10GB and OS X on an internal 20GB, both Western Digitals.
To make a long story short, I kept getting disk errors upon running fsck. I tried reformatting the drive and reinstalling, which would work -- but I was only doing the "initialize drive" option without doing the long, boring, zero-all-bytes format. When I finally did get around to doing the long format, it would error out every time.
I ended up yanking the offending drive out of there, muttering a few choice words and completely getting rid of OS 9 on my 10GB -- I never used it anyway. Reformatted with zero-bytes option, installed OS X, and haven't had a problem since.
The ironic thing is that this damn 10GB is four years old and keeps chugging along, while the 20GB is two.
The double-irony is that I'll be doing the complete reformat and reinstall AGAIN when Panther gets here... don't wanna do the upgrade route, and I'm so damn good at loading a machine now (I regularly service and fix ten of them) that I can have a complete OS X installation, complete with all fonts loaded and all programs loaded (Adobe suite, Macromedia suite, Quark, Suitcase, Office, and all updates) with the GUI tweaked to how I like it in about 2 hours.
I think we've all learned to keep a good backup or two laying around just in case... you never know when they're gonna go...
