I have a similar problem with my '15 JKUR. I do not have an Atlas, just the stock 4:1 rubi t-case. I feel like it usually happens when I'm on an incline, go to give it some skinny pedal and there is nothing there, nada tostada, but a low RPM grown and zero power.
Last time I checked and all of my temps were within range. I've always chalked it up as having something to do with my supercharger and the tune. It is mighty inconvenient as well as utterly frustrating.