I would check on the tightness of ALL of the bolts on the tailgate (tire carrier, spare tire, tailgate hinges, etc.). Also, check the exhaust hanger in the rear. None of my Jeeps (2 early 90's YJs and an '03 TJ) have ever had a rattle that didn't mean that something wasn't right/tight. I would take it to a different dealership also, if it's feasible for you, or make sure you have it in every week until you get it resolved at the one you are currently using! Make sure you and the service manageer are good friends by the end of this, even take him doughnuts every Saturday if you need to...

Good luck, and keep us updated!