yea sounds like the front latch microswitch, it's not connecting so the car always thinks the top is half open so it prevents the windows going full up. When the top is fully open the rear microswitch is tripped and it knows where the top is again, so the windows work. When you remove the battery and reconnect, it still thinks the top is half open but doesn't know where the window is so, drops them again to be safe.
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