It definitely could. Here's a recent thread for more information around that:
https://www.ecodieselram.com/forum/threads/running-a-tune-and-going-to-a-dealer.1276/
It's not uncommon for a dealer to "update" (flash) the truck to the latest software. In my previous vehicles it was pretty common. It really depends on the dealer.
You would need the proper tools to be able to tell if it was flashed or not.
Try removing the negative battery cable for a bit. Otherwise, it might be a defective unit and/or need a software update. I remember someone having a similar problem and a software update resolved the issue for whatever reason.
If you're under warranty take advantage of it. :)