I had a Wrangler Rubicon and Jeep knows that these are tough machines with numerous issues such as their clutch.
With 5k miles I would get this noise when shifting between 5th and 6th gears and i brought it back 5x times to get the same answer..."it's a Jeep thing".
I asked to know when the factory rep visited the dealership (most companies send them out on request) and we met that day, he said I needed a new clutch when all 3 rep, me and the service manager went for a ride...this MOFO (service manager) said..I never heard that noise...grr well I had it fixed, good luck and stick to your guns