You may have to re-sync the windows, if the battery was disconnected there is a process to have them "re-learn" where the stop points are. Check your owner's manual but I believe if you lower the window and hold the button for a few seconds until it clicks, then do the same when you raise the window it will reset.

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Marty D.

2013 C300 4Matic
1984 BMW 733i
2013 Lincoln MKz