At this point I think you should get Applejack...
http://www.versiontracker.com/dyn/moreinfo/macosx/19596
After installing, reboot holding down CMD+s, (+s), then when the DOS like prompt shows, type in...
applejack AUTO
Then let it do all 5 of it's things.
At least it'll eliminate some questions if it doesn't fix it.
The 5 things it does are...
Correct any Disk problems.
Repair Permissions.
Clear out Cache Files.
Repair/check several plist files.
Dump the VM files for a fresh start.