Not 100% sure but it might need to be set.
im prety sure the motor will always try and run. If your window is at the top and you press the close button it will still try and move it, you hear it clicking etc.maybe it is something with the regulator?
My suggestion would be to take the window back out and re fit it. It could be an allignment issue. They usually go back down when theres something in the way (on the later models) The motor on mine went and i had to refit it and had to allign it a few times so it would sit properly.Hope this helps!!