Someone PM'd me about this, so I'll post the response here. Here's how I got it fixed, FINALLY:
For me it wasn't the sub, or any of the sound gear. I told the dealer this but they refused to listen.
Mine got so bad that I literally wanted to crash my car into a wall. My girlfriend was even a bit apalled at the noise. One weekend I decided to track it down and fix it myself. I noticed it was the top plastic deck lid (where the speaker grills are). I noticed it didn't quite fit right back there and the back of it had enough room to rub against the rear window. NOTE: This can all be seen/heard from inside the car not inside the trunk. Sit in the backseat, turn around, and press on various areas of the plastic deck lid until the noise is heard. For me it was on the driver's side area by the glass. Pressing it up and down would reproduce the horrible noise.
I then decided to take the deck lid off and try to reseat it. In the process I broke some of the clips and made it even worse. I then stuck some towels in between the window and the deck lid. It looked real ugly (especially since the towels were white). You could see it from outside the car, but I didn't care, it provided a cushion for the decklid against the window. The noise stopped. I took it to the dealer about a month later and just told them to take a look at the towels, and that the towels fixed the problems.
They ordered me a new decklid and installation clips for them (~$200). I told them I broke it trying to fix it, but there was certainly a problem with it before. They still covered it under warranty, and now with no towels it doesn't rattle. Took a few tries but that's what it was for me.
Now I have a small rattle in the passenger's front door, trying to figure out how I can find it.
)LMAO!
