Ok, here's my two cents and I could certainly be wrong but I had this happen to me and it was my own fault, so that's where my recommendations to find the cause comes from.
My wife's Golf diesel was a pretty quiet car until I decided to give it a good bath and detail. I waxed every bit of paint I could find and used something, I don't remember anymore what it was but it was some kind of rubber protector product, on all the door gaskets. You know the kind that is supposed to keep the rubber pliable. Her car was looking quite nice inside and out!
Then I noticed while driving it out of my driveway that there were noises never heard before. They sounding like someone rubbing a balloon against their hands or a wall, though more subdued. The noise only happened when going slow over uneven surfaces, like when entering or exiting a driveway, parking lot, etc. Ugh, If I rolled the windows down and grabbed the window frame and pushed up or down on it, hard, I could reproduce the noise exactly. What had I done?
The door gaskets are of course to seal out the environment but they are of a material that when pressed against the door sill, which is painted, the will normally not slide, they keep their grip while the door moves from normal body flex. However, if they lose their grip, they will rub and you will hear it. I believe this is what was happening.
I had my wife drive while I sat in the back seat and I could see the door frame gap width change as she drove around the block and in and out of our driveway and I could easily hear the noise at the door. Word of caution..do not put your finger in that gap while the car is moving in order to feel the gap width change
Like I said earlier, I could be wrong but I would bet this is what you guys are hearing. Its pretty common for a dealer, detail shop and owners to want to preserve and protect their car by waxing or using some other protectorate, both on the paint as well as the rubber gaskets around the car. Once done, its very very difficult to remove it and get the car back to normal. If this isn't the case and you know for sure no one has ever applied anything to your car, then its time to do some testing to see what is causing it. You can't fix it without knowing what's causing it, unless you are blindly lucky in which case you will never really know what you did
- Roll your windows down and with the car off and in a very quiet place, grab the door frame and move it aggressively in all directions. Listen for the sound and pay attention to the gap between the door frame and the car, you will want to see it change widths so you know you are moving the door.
- You can use the painters tape or pieces of paper to put between the door gasket and the car and close the door on the paper. Then grab the window frame and repeat the test or take the car around the block.
- All this applies to the rear hatch as well. Noises are strange as they normally originate away from where you think you hear them. Taking the car to the dealer may be an exercise in frustration for you and them and you'd be without your car for too long while they do little more than what you would do at home. You can talk with them though, its possible they might understand what you are referring to and be able to give you some advice...maybe.
I think this sort of thing is best dealt with at home by you and if you find the cause and its something wrong somewhere with the car, then you can take it to the dealer. Grab a couple beers, have a friend come over and go at it.