I may be wrong, but I'm pretty sure all of the Lexus' come with a safety in them that if something gets caught in the window it will automatically drop the window to the half way mark. It sounds like something is causing the rear window to bind on it way up and triggering this safety. Another posibilty could be the windshield motor isn't installed/adjuseted correctly - I wouldn't know for sure on this without taking the door apart. I haven't had this problem on my GX470, so I haven't taken the door
liner off and examined the setup. I do know on my GMC the just rivet the motor in place - the fix? drill out the rivets and redow the entire motor installation assmbly - not fun.
Who did the work? If was the dealer, I'd be taking it back.