This isnt the first thread Ive read about a Chrysler having issues when uploading a transmission tune. I took a risk when I did it with my DiabloIntune but luckily didnt have any issues what so ever. Apparently the TCM dont like to be reprogrammed which isnt just on Jeeps, but chargers, 300s etc all have had issues similar to what you're getting when a tune was uploaded, just something to keep in mind.