You are probably thinking of the auto transmission (42RLE)... Nothing really wrong with them, but your tire and gear ratio choices can make the overdrive gear not function as well as designed by the Jeep Engineers. It is an electrically controlled trans vs. the older 3 speed (32RH), which was a hydraulic unit.
Got the 06 SE with 6spd manual tranny and I have not had any issues nor heard of any except I have the 4cyl which I love but I'd recc 6cyl. Great Jeep you'll love em and if you want the full pkg get the Rubi which comes with an SYE and lockers and better axles.
42rle were not as good as the 32rh, they have a much lower heat tolereance, so if you go mudding don't spin your wheels alot trying to get out, that thing will fry. they are still a good tranny, just not as good as the 32rh
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