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The window needs resetting.
Get the window down to it's lowest position and hold the button down for a few seconds,then get the window up and hold the button up for a few seconds.This will teach the control unit it's parameters and all will be well.
You need to to do it if the battery has been disconnected or flat.
Currently in Lagdti's garage:
2004 Saab 9-5 HOT Aero and a 2001 Audi A3 1.8 Turbo