There is a technique to relearn the auto up/down feature after replacing or disconnecting the battery. With the ignition on, hold the switch until the window goes all the way down, keep holding the switch and you will hear a faint click. Then lift the switch so the window goes up, keep holding the switch and you will hear another faint click - this should now have relearned the upper and lower limits of the window and your auto open/close feature should work again.
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