'Repair Permissions' doesn't repair permissions?

Question

As part of my efforts to solve this problem:
http://discussions.apple.com/thread.jspa?threadID=296986&tstart=0
... I copied my entire user folder from a recent backup to a mirrored volume.
Unfortunately, instead of using a proper backup program like Retrospect, I foolishly used the GUI to simply drag and drop my user folder to the mirror and later, to "restore" it. Apparently, that caused all of the permissions all over my ~/ folder to be borked beyond belief.
I have tried repeatedly using repair permissions, but it hasn't changed a single permission setting on any file or folder of my user folder, as far as I can tell. My account is the admin account of course, although Disk Utility never asks me to authenticate when repairing permissions.
I have other user folders on the machine which are working fine, and I have managed to fix some of my file & folder access issues by duplicating the permission settings seen on their folders (substituting my user name where appropriate, obviously).
One of the more frustrating issues as a result of all this is that anything I download with Safari goes to the correct download folder, but is not visible in the GUI. I can find it by searching with the Finder, and permissions appear to be correct for the file, it just isn't visible in the GUI.
Anyone have any ideas why Disk Utility isn't repairing permissions to their correct states, and also why downloaded files might be invisible to me despite them having the right permissions (and the downloads folder also seemingly having the right permissions)?

Answer 1

Repair Permissions only works for the OS and installed applications. It does not fix permissions on user data, only on files referenced from the receipt files (in /Library/Receipts and ~/Library/Receipts).