If it is going down the same as if the top was opening, it may be a problem with the top latch microswitch. Open the latch for the top and poke something in where the little hook latches. Push it in all the way and hold it while putting the window all the way up. Does that change the operation of the window?
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I am not an attorney, mechanic, or member of the clergy. Following any advice given in my posts is done at your own peril.
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