i had a stereo head unit installed in my scion tc recently and after the installation i could no longer control the passenger window from the driver side controls. a quick google revealed that the ECU (engine control unit?) needed to be reset. the instructions i followed were disconnecting the negative terminal of the battery for about 15 minutes. then reconnecting it and letting the car idle with no AC, headlights, or stereo on.

i don’t know if the idling step is necessary or not, but it worked for me.

source:
http://www.scionlife.com/forums/showthread.php?t=207683