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When you say you replaced them roof switch, do you mean the center console one that lowers and raises the top? My guess is the latch micro sensor located above the rear view mirror thinks the top isn't latched so it keeps the windows lowered an inch or two.
Try this. With the top closed and unmatched, try pushing with your finger or a pencil on the spot where the latching arm would go when it's closed. If the windows go up, you'll know where the problem is. The problem still may be there even if the pencil test doesn't make a difference. But its worth a try given it takes just a minute.
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