Sounds so much like my problem. But mine is more consistent, happens to both windows by the same amount, and only when the top is closed.
I read somewhere that your symptoms could be the microswitch at the door handle that is going wrong / stuck? Think suggestion was to use the key on the door, turning to lock and hold for a few seconds, then turning to unlock and hold for a few seconds, and do this a few times.
I'm starting to hate relays, so you might want to try pushing all the relays under the right side footwell to make sure they sit in tight.
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