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Non original window electrical systems tend to be noisy - thats why they are cheap. It all about the quality of the motor and its associated drive gears. I have seen it on numerous occasions. Sound proofing the door may help very little - you could try sticking some gaffer tape round the motor and mechanism. The noise is usually transmited via the window itself so you may just have to live with it.
Currently in madnoel10's garage:
Honda Civic 1.4l