Start up with the OS CD (plug in the adaptor cable to the book and a power source. and - not clicking on the installer screen, go to the Installer Menu and select Disk Utility. Click on the second hard drive in the side bar at the left, then click on repair drive.
Watch the activity screen. If it does any repairs - you will need to click on the Repair Disk button a second time after the first pass is done. The object is to make sure it finds all the problems and repairs them. You may need to hit that button a third or fourth time to get no references to repairs made.
Now click on Repair Permissions.
When that is done, quit Disk utility and restart the computer.