i can only speak for my situation (front o/s window) but i had to remove the inner door card and re align the window to the runners. basically what had happened is that when i had the door controller replaced they didnt put the window on properly so it slanted one way and put pressure on the edges. you will need to loosen the window and align it properly, tighten it then test, with a bit of trial and error you should be able to sort it out. i also lubed everything up while i had the door card off.
it was one of those things that the dealer didnt want to / couldnt fix....