We had ours in at least five times, including them sending it to a body shop and them tearing into it to see. Apparently there was a rubber spray on seal that was neglected to be placed between the seams of the posteior segments of our Patriot. Luckily for us, we have a small town dealer that really prides itself on taking care of their customers. They intervened on our behalf, after Jeep tried to tell us (in a very *****y way) that it was not their problem. Basically they offered us a sticker for sticker swap on the wife's 2008 Liberty.
Best of luck. Get your dealership involved, and mention that you are not scared of seeking legal counsel.