Did the dealer show you how to put down and put back up your soft top?
I would take it back and have them do it again.
My soft top JKU is near silent. This is my 1st Wrangler and I am surprised at how quiet it is.
The top has only been down twice (hot humid rainy in FL) since my purchase 5/1/2012. The dealer said if I had any problems including having questions on the top to bring it back in and they would go over it with me.
If you don't want to go to the dealer here is a link to the proper way to put down and put back up your soft top. Give that a try and it may eliminate the sound. If not take it back to the dealer.