This is out of interest rather then looking for a fix to a problem.
What actually causes permissions on Mac OS X Systems to become messed up? Its an easily fixed problem (i.e. there's a quick and easy fix via Disk Utility) but its something I'd encountered a few times doing support in a Mac-reseller store without actually understanding the causes.
I'd guess that part of it is due to some applications not playing nicely, but what else might be the source of this issue?