Daniel, the Jeep issue maybe inside the ECM. GM had issues with wiper motors doing the same thing, ended up being a bad solder joint on 1 or 2 spot on circuit board.
My Firebird had an issue with the BCM, the radio would go off/windows wouldn't work. Hit a bump and back on. I pulled BCM from under dash, re-solder a couple joint points, been fine every since.
Wonder if Jeep had an issue like that?