mine had this problem. it ended up being the motor cable for the upmotion. it's working against gravity and window guides, so if the cables are not properly slack, then the motor will show that the voltage is too low and won't raise the window.
but since you're getting the window to raise by swapping the connections, i wouldn't suggest taking apart the motor and checking the cables.
wanna know how i fixed mine?
two short 2X4 scrapes shoved under the window and took the cable. ;]
but this is usual for any old electric windows.
i believe it's mainly resistance. the harness/ circuit that ends up at the windows is losing too much power before it gets to the window motor connections. when the car's brand new, the wires and connections are too, so it's easy to push that much power through.