The windows do go down as normal, push the switch and you get the endless beep. I was going to try the allen wrench trick with the rear top latch to see if it was to tight or something, but the dealer broke the trunk, so I couldn't try it.
I went out and bought the deluxe warranty on it to cover everything, I really wish I could take it to the Benz dealer around the corner, they could probably fix it in 5 mins.
I've considered taking it to the Dallas area to have a look and I just happen to have a kid that lives in Denton, so thanks for the tip.