You may have a Smartop module in your car as one feature that can be programmed is to raise the top and have all windows go up but the the driver window goes only 1/2 way up then down.
Easy way to check, turn on the key (don't start) and hold the door lock button on the dash, for 10 -20 seconds. If nothing happens you do not have the module, if the turn indicators on the dash both flash then you do have one.
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