Transmission runs on engine oil. My Rubicon was overfilled and I had a similar issue along with a leak at the oil tank caused by the over fill.
The transmission is a variable swash plate, fluid coupled. No belts, no clutch, no "gears" if you will, it's a constant variable. Electronically controlled.
Oil filter is a PIA the get to, and is an internal cartridge type. I did it myself a few times, dealer has done the servicing since I had my problem.
Good bike though, mine is a 2001 and still going strong.
I would start with the engine oil / filter. If is hasn't been changed, low or high, gotten water in it, etc. If that is ok I would try to run it on the manual mode and see if it makes any difference.