When you take the door panels off, you have to do a much longer reset procedure. If I remember correctly, you hold the button down for about 20 seconds. Not in the automatic position, just like you were rolling the window down without the auto function (first click). Then, roll the window up under the "manual" setting and hold for another 20 seconds.
The first time I pulled the door panels to work on replacing the speakers, I hooked everything up and the windows wouldn't roll up. I about crapped a brick because there were storms coming. Once I did the long reset, it worked fine.
edit: Seems like it might be 15 seconds.
automatics windows don't work correctly after door speaker swap?
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