I got similar trans shifting weirdness after the 5 Star tune. You're saying that doing the battery reset fixed the shifting?
If I flash the tune back to stock it shifts perfect. If I flash to another tune the shifting is weird. I'm working it out with 5 Star right now.
anytime you mod or change anything on the truck do a kam/idle reset.
load the tune in. then let the truck sit. disconnect the battery negative side first. turn on the headlight to drain it. no they shouldn't come on. leave for about a min. reconnect the battery with the headlights off. positive side first.
start the truck with the ac, radio and lights off. let idle for 15 min to operating temp. turn on the radio, ac and headlights. idle another 5 min. then with every thing still on and your foot on the brake, put it in drive for 5 min.
then drive the truck normally in sport mode for better learning.