Blank permissions after upgrade

Today, I upgraded to 7 on my Asus laptop with the free upgrade that came in the mail. After launching World of Warcraft I noticed a problem, that some of the subfolders in the installation had no permissions assigned to them, and as such the program couldn't access them. I also noticed that various other folders on my hard drive had missing permissions. I can right click on the specific folders and go to security and add permissions to them, but any subfolders that have the same problem come up as access denied when I try to apply the settings. The same thing happens if I try to modify the permissions on the root drive (C:), it starts modifying permissions of the subfolders and files but once it hits one that has blank permissions it says access denied. How can I set the permissions on all the folders at once?

Thanks for the reply, this should be added to the common problems sticky. It's currently going through all my files on my C: drive, and it's already been through some of the folders that had the problem, so I assume it's fixing the problem.