Magzy, You certainly have been very unlucky with your kit and I'm in total agreement with Leslie on this one. If a simple cure cannot be found, then I too feel that the wheel should be replaced under the warranty as the fault must be somewhere within the wheel if it's not crossed wires in the harness.
As I haven't seen the wiring on the external Pies, I don't know what connector are used, or what the chances are of a couple of wires being inadvertently crossed during the manufacturing process, but I guess it could be possible.
It could be easy to mix up the three separate ends of the windings, as these wires as they are plain copper wires without coloured sleeving.
The internal controller has short lengths of coloured sleeving on the ends to show which is which, but I presume that these wires on the external controller Pies are soldered directly to the three coloured phase wires which exit via the axle.
If the the colours for the phase wires or the hall sensors have somehow been mixed up somewhere between the stator and the controller, it should be possible to find the correct configuration by following
Muzza's suggestions.
Did you by any chance take any close up photos of the wiring connections while the wheel was dismantled? as this might help to check if the hall sensor wires are in the correct sequence at he wheel end.
If you click the image to enlarge it, the colours of the hall sensor wires are more obvious.
I think your concerns about damaging the replacement are completely justified, and I personally would not want to use a motor that was making loud noises and was not running correctly!
If you try the different wire combinations suggested by Muzza and find no combination that works correctly, then Tom/GM will have to do something to rectify the fault!
A short video might be enough to convince Tom that there is definitely a fault with the running of the motor.
Please keep us informed of what happens.
Alan 
