If you do a search, stlwagon has posted the fix for this. It's one of those things like programming a key or fob where you stand on one foot, turn around twice, push a button with your nose six times, etc. and it recalibrates the window. Might be in your owners manual too.
Edit: Found his post.
To reset the windows. Roll them down and hold the switch for 2 more seconds. Then roll them up and hold the switch again for 2 more seconds.
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