Hmmmm...not good. You didn't mention doing the following (which will help more then the permissions thing)...Try using Disk Utility to do a Disk Repair, as shown in this link, while booted up on your install disk for OS 10.6.8 and under. If you are running 10.7 or 10.8 run Disk Repair from Disk Utility on your Recovery System. It shows you how in the link.
You could have some directory corruption. Let us know what errors Disk Repair reports and if DU was able to repair them. This could just be a start in repairs and you may need a better utility to finish the job.
Then see if you can Repair Permissions.
No need to report any Permissions errors........we all get them.