Doesn't make any sense to me but it may help the troubleshooting efforts of others if you will open the door while rolling up the window and noting the door position when the window stops. If it stops as soon as the door is cracked open, it may have something to do with the door status switch (wild guess).
On modern, computer-controlled cars, it's always possible that unplugging the stereo could cause a spike and mess up something.
If no one comes up with a solution soon, I'll look through the FSM and see what I can figure out.
Good luck.
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