Okay well I'm not expert on permissions. I know that taking ownership of some system files can cause issues if changes are not reverted after working on some system files. It looks like you've figured out how to revert permissions. I've seen issues with a self replicating application data folder for example.

Junction Box can restore default permissions on specific folders. See Post #6 here:

Stop Application Data folder replicating? Solved - Windows 7 Forums

Download Junction Box

There's no need to run that if you're not having problems. It's just posted for information because you should be getting "access denied" on that folder.