The Directory on the Hard drive can get messed up. In 10.4, the cleanest way to deal with that is to boot from the Installer DVD, but do not Install. Wait a quarter minute for the menuBar to be drawn, then choose Disk Utility off the Menu.
Chose your Hard drive by Hardware_name and ( Repair Disk ).
When you are done, choose Set Starup Disk, and use it to set your startup disk and then Restart.