The sunroof on my car does the same thing, but I can get it to close by pushing the button repeatedly about 100 times. Try pushing the button really fast and see what happens.
Also, if you know how to take your door apart, check all the contact points on the switches. If there is corrosion (greenish stuff), then it could just be causing a bad connection. Get some sand paper and sand it off. Might not be the motor, considering it goes down.