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Anytime you replace the battery or disconnect the power in a Toyota, Lexus or Scion you will need to do the re-initialization of the windows, and also the sunroof motor.To do it, its very simple and these are the steps:
1. Turn the ignition to the ìONî position.
2. Push the close side of the moon roof switch and hold for 2 seconds after the motor stops.
3. Verify proper operation.
I also attached the Tech Tip from Toyota.
please try this and let me know what happens. If this does not work, there is one more thing to try. When you push the "Close" button and hold it after the sunroof has closed and the motor has stopped, you are telling the ECU where the "end travel" is of the sunroof.