ginagary,
We've towed 8 different Jeeps for over 30 years and as of yet, yet to have any tire issues what so ever. I've read on here and, a couple other forums about tire issues on Jeeps when towing. I think it's an extremely rare condition as, about 99.9% of the folks towing them don't experience any problems.
Now, as you yours, since it is a rare problem, it's pretty hard to diagnose your exact cause. You say it's been aligned. Well, that sort of takes that out of the equation. I don't think tire balance could be the problem but, you never know with these darn Jeeps so, if you haven't done it, I'd head on down to your local tire dealer and have them checked for both balance and, "run-out". Run-out is, the tire being out of round or, like an egg shape.
Could that be your problem, well, not sure but, not likely. You say your tire condition is "Flat spots". Do you mean "cupping" or, multiple odd shaped spots, all the way around the tire(s) or, do you mean flat spots as in only on one section of the tire(s).
How is your tow bar angle? Is it close to fairly level when hooked up to the coach? Not that, that makes all that much difference in any sort of tire wear. We're presently towing an '03 Rubicon and our difference is about 6". I know, I know, (for all you "PERFECT" tow bar angle police out there)that, that is not the optimum and, sooner or later, I'll get around to correcting that situation.
But, as long as the OP has the steering unlocked (if his year model has a steering lock), the transfer case in neutral which, I'm assuming he/she knows all this and, is doing things correctly, and, as stated, has had the Jeep correctly aligned, tires balance, checked for out-of-roundness, and all steering components, tie-rods, drag link, panard bar connections, shocks, wheel bearings etc. are in good shape, then I'm at a loss too as, like stated, we've towed many of them and have never had or experienced any odd tire issues.
Good luck and please post what you find out, if you do, what the problem was/is.
Scott