I found something interesting in Apple's support info: Should I start up from a Mac OS X install disc to repair disk permissions?
When possible, disk permissions should be repaired *while started up from a Mac OS X volume (hard disk) that contains Mac OS X*, instead of a Mac OS X installation disc. Mac OS X software updates may change permissions on some files to improve security. *When this occurs, the version of Disk Utility on the Mac OS X volume is updated to account for the new permissions.* Running Disk Utility while started from the Mac OS X volume ensures that the changes made by software updates are preserved. I don't know how it affects anything else though. Nora
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