there used to be problems with the tranny but i think it is all updated and fine now. when i dropped the tranny out of my 03 i got all the updated parts(i beleave i got the 05 parts) and everything was fine after that. i never ran in auto on my rubicon, i never liked how it shifted. the D1 is used for speed, and the D2 is used for torqe. i think the new rubicons have all the bugs worked out of them and are good to go. if you do go on to buy the rubicon i would give it a test drive first. i never really cared how the auto felt on it so i would make sure you liked it before you bought it. some people like it and some people dont.
-Aaron
-Aaron