Should you suspect that the Motor Unit is faulty, then we would initially suggest you check here.
Otherwise, you can test the motor unit as follows. Undo the 4 screws on the Motor Control Unit and remove the lid.
Check that the cord runs behind the internal microswitch lever as shown:
Disconnect the wires then use one of the battery packs to test as follows:
Connect the black wire from battery box to the red wire from motor control unit, and the red wire from battery box to the black wire from motor control unit. The motor should spin (clockwise) such that the unit draws in the cord. It should stop if you push up on the lever protruding from the underside of the motor unit.
Now connect the red wire from battery box to the red wire from motor control unit, and the black wire from battery box to the black wire from motor control unit. Motor should spin (anti-clockwise) but only if the cord is under tension (i.e. pull the cord tight as if it is supporting the weight of the door such that the cord pulls the switch bar inside the motor unit forwards). The motor should stop if there is no tension on the cord.
If these tests pass, then your Motor Control Unit is working properly.