Sorry for the late reply, my wife had our baby
Since you can run it from the desktop it sounds like it is a permissions problem, since things ran from the desktop dont normally need admin rights.
I wonder if you might have something on the system that is continually changing or messing with permission on the system, a virus would do that of course, but other programs could as well.
The commands you are doing is what the repair is doing and yet later it is messed up again.
What tools have you used to scan your system with?
Shane