Take a look at
this Apple Knowledge Base article. In particular the last paragraph which is titled
Should I start up from a Mac OS X install disc to repair disk permissions? That article was spot on! By running repair permissions from Snow Leopard startup disk (10.6.0), I lost any permissions updates that might have been contained in 10.6.1. I have since run repair permissions from a Disk Utility app that is from 10.6.1 to cure the potential problem. Again, thanks a lot!
