Update, after checking the operation on the window motor I have found that it does not seem to sense when it reaches the bottom, and tries to carry on going down with the full power of the motor. The wiring diagram doesn't show much at all, but when I stripped the motor down there are two sensors which sense rotation of the motor and give feedback to the control unit. So, I've plumped for a motor in the hope that this is the problem. It could also be the control unit I suppose. Will fit parts when I get them and update.