ryanw said:I have been doing heavy unix administration and engineering for a good portion of my life of all flavors of unix. I have never seen permissions just randomly 'flipping around'. Sure, you can blame a 3rd party product for mucking around in the file system and changing things. The real question is what does 'repair permissions' do? What subset of files is it querying as the 'authoritive source' of information of how the permissions should be set? And if this thing exists, why can't 3rd party developers muck that up too? Very bizarre...
I believe it only fixes files that belong to the base Mac OS X system. It references what the originally installed permissions should have been. I don't know where the master list is. It will also fix files with permissions that are set to an invalid number. (e.g. owner/group settings to an invalid uid or gid which is never really valid.)
Permissions are sometimes flipped to an incorrect setting by installer programs. In the UNIX world, people didn't install software under various "admin users" with various third party installers (they're usually install scripts run under sudo), so it's not as common. It does happen sometimes though.
Fixing permissions is a bit of a red herring for most problems, often people restart after fixing the permissions, which fixes some problems by cleaning out the /tmp folder. There are a few permission-related problems, but MacFixit's recommendation of repairing your permissions before and after updating your system is a bit ludicrous as well. It's not a magic bullet.