You mean Snow Leopard, or Lion? Booting with the C key is for booting to a DVD, don't bother with that.
There will be permissions that can't be fixed, that's not an issue.
If you lost your boot drive once, it could be on it's way out eventually. Run Disk Warrior to rebuild the directory, and if this fails, the drive is about to die. Reinstalling the OS won't help anything.
Run Disk Utilty like you did to Repair (ignore Verify, waste of time). Run Disk Warrior. Do both once a month for good house keeping.
Also highlight each drive one by one on your Desktop. Command-i will give you the Info window. Look at the Capacity, and make sure the Available drive space is at least 15% of the capacity.
I'd not run Onyx for many, many, many reasons. It is not doing anything to actually help your system. The only reason Onyx or Cocktail should be used is if you turn your computer off at night, or it goes to sleep at night. Then it doesn't run it's UNIX system clean up routines. These won't hurt your system if they never run, but using something like Cocktail or Onyx to run them manually during the day doens't hurt. Just do NOT let Onyx or Cocktail do anything else but run the Daily, Weekly, and Monthly UNIX routines! Everything else they do is 1- a waste of time, 2- can potentially mess you up.
Here's a blog post of mine you may be interested in.