Each window has a pressure sensor that must be reset each time the battery is disconnected. My wife has an '04 RX330. According to the owner's manual for '04, to reset the pressure sensor for a window, bring the window down half-way, using the control on the same door as the window and then raise it back up, holding the up position on the control for 1 second after the window is all the way up.
On the '04, this brings window control back to driver's side module.
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