You just may be stopping on the bad part of the motor that has the short. Most people have the window open or closed so this is why your short in the motor windings or bushings may only worse in the up or down positions cause the window can rattle the motor when it is partially opened easier.
I am guessing at the travel stops of the motor assembly there may be bad internal switches.
My Window has the same issues, I fix it by slamming the door.
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Mark V
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