The Apple Installer / PackageMaker tools make it perhaps easier than it should be to create a package which will install and mess up permissions. It *looks* easy enough to create an installer package--hey, just fill in these fields!--but there are a lot of gotchas that aren't apparent through that esay interface. There are a number of good tutorials on the web outlining these gotchas, and Apple's documentation looks very thorough--but it seems so easy that many may not read the docs or search for the tutorials.

I've also had Backup once fubar the permissions on /tmp 2/3 of the way through a 7 CD backup and die, so applications (or perhaps OS bugs) can sometimes mess things up, too, but predominantly it seems to be poorly-created installer packages.

Bottom line, if you install software from vendors other than Apple, you should be running repair permissions--and running permissions before and after OS updates seems to help them work properly, too!