Suggestion from someone who doesn't quite know what he's doing so excuse any inaccuracies:
This seems to be similar to the last comment, but I'm not quite sure. I had a couple of problems and shut off the computer without letting OS X clean itself up. On the next start, I was getting hung up on, I think, "checking system disks" or something like that. I booted into OS 9 and ran Disk First Aid. When I booted back into OS X, it started normally (no delays). I didn't do anything else ... no reinstallation or anything else.