Forgive me if I am suggesting something very basic, but have you tried repairing permissions using DiskUtility? If you are unfamiliar with this procedure, this is what you do:
Go to Applications/Utilities/DiskUtility.
Click on the 'First Aid' tab below the toolbar.
Select your Mac Hard Drive partition from the list on the left.
At the bottom of the window click 'Repair Disk Permissions'.
If you get any message saying "Permissions differ on
", when the scan is complete repeat until no error messages appear (or the only messages are "We are using special permissions on
" which can safely be ignored).
If your problems persist, restart from your installer disk (see below) and proceed as above but instead of clicking 'Repair Disk Permissions' click 'Repair Disk'.
Note: If you can't access DiskUtility on your computer, then start up from the installer disk (restart with the installer disk in the drive and hold down the 'c' key until you see the Apple logo). When presented with a window asking which language to use, click 'English'. When the next window appears, do not continue with the installation but go to the now available top menu and under the 'Installer' heading select 'DiskUtility'. Proceed as above.