if you could some how place a speaker near the location it sits with the door panel on, without installing the door panel, and then playing some music you maybe able to recreate the problem, so you can pin point it and fix it with ease since the door panel wont be in the way hiding the problem. also when you lower your window it maybe stiffening the interior of the door to the point its eliminating the problem, and when rolled up then it allows for the door to flex more an for the noise to be created.