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Try this. Hold the switch when rolling down, keep it held for 5 seconds after the regulator stops, then hold the switch on in the up direction and keep it held for 5 seconds after the window closes. This will reset the timing on the regulator in many cases for express windows.
Take the motor off and cycle it, there use to be a nice online list of re-set notes I can not locate it any more :( I know if you search here hard you can find it.
Had the same issue with the late model Prius and I never power a vehicle up with any switch or device unplugged. Gave up and told the customer to take it to dealer. (Had an OEM glass as well). Used the tried and true manual reset but did nothave time or patience to do the motor reset.