Ask your shop guys to do a phantom current drain test. That will tell you if there's something draining the battery when the truck is parked overnight. Not an uncommon thing w/newer vehicles. When you park for the night all the computers should all go to sleep after a few minutes, but sometimes something keeps waking up the computer, and when the computer wakes up it uses much more current than when it is sleeping. One common causes is the wind is blowing on a door, which makes the computer think someone is getting into the truck to start it, so it wakes up. A door switch malfunction, same thing. The phantom current test would catch this. And make sure your cell phone or other personal accessory isn't plugged into the vehicle overnight of course, as that could put a drain on the battery.
Not driving the truck enough or for enough miles, as mentioned above, could cause this. In that case what you are seeing is normal behavior. It's saying it can't properly charge the battery and do the auto start/stop function, so it is deciding to skip the latter and just focus on keeping the battery charged. New vehicles that have a lot of electrical gadgets in automatic use don't work like those of the past; the new ones use a complicated computer-assisted battery charging algorithm to try to get the best compromise of a charged battery and the other gadgets working.