the manual has an anti stall feature that makes it kinda prone to stalling ive found. do this, go out and try to get the car rolling without using the gas, just clutch only. you'll find the jeep actually gives itself a bit of gas to stop from stalling out. when you try to feather the gas (the way you normally would with a stick) it cancels out the auto gassing, and seems to stall it. makes it a pain when youre in 2wd trying to do things slowly, like back out of a spot in a parking lot. awesome on the trail, or when youre stuck in traffic.
but seriously, try the gas-less driving thing. so cool.
*edit* didnt notice you mentioned you knew about the anti stall. might mean your clutch is worn or you've lost some of the clutch pedal fluid. or might need a reflash