XP Home Permission Issue

I am helping a friend w/ a weird XP Home issue. He is getting an error that says something like “Windows cannot access this file…May not have correct permissions for this directory, file etc..” when he tries to open Outlook, or MS Word or really any program it seems. However, he can open a Word document in the My Documents folder and Word will start right up and load the document.
Not sure if it is related but we had just finished getting rid of a virus he had picked up. We used AVG Anti-Virus in command line mode to finally get rid of the bug. Any help would be appreciated.