I would suggest you use a tail light bulb or something similar to test with. You could have 12v, but not enough current to run the motor.
For example, you could have a wire broken all the way through except for one strand, and the voltmeter will still show 12v, but that one strand of wire will not carry enough current to light a light bulb--or operate your window motor.
As suggested earlier, you could also have a bad ground.