An Australian AppleTalk article talks about why Repairing Permissions is Useless:
Despite what Apple’s Knowledge Base Article says, Repair Permissions does not repair permissions on any third party software (or any Apple software outside of the Base System). I just checked this by changing the permissions on FontAgent Pro and then repairing permissions. The permissions were not set to their correct values.
What Apple’s Knowledge Base Article says
Note the limitations in Apple’s instructions. For example, I would venture that installing Office causes it’s permissions not to be repaired (Drag the folder to your Applications folder) Most software I install do not use the Apple preferred package file install, which places a bon file in the Receipts folder .This is important, as Disk Utility only checks the Receipts folder for bon files to repair. Not the Office 2004 folder, which did not use the Package file install procedure. This becomes, according to the article, Apple’s fault.