I would contact the person who made your tunes and talk to them. There hve been people before with tune issues, their tuner sent them a new file and all was well. I also recommend looking into Gearhead tuning... I LOVE Matt's tunes
Granted I am relatively new to the 6.4 after owning my 6.0 for 4 years, but I agree with the above. After searching for over a month and reading a ton of reviews it sounds like Gearheads tunes have way less issues than most others on the SCT. Now that isn't bashing anyways, just that their SCT tunes seem to be the most reliable option for the 6.4 out there. On top of the searches here, I emails Matt/Larz several times, probably more than I needed to because I wanted to make sure I was making a wise investment in my custom tunes and had ones that would 100% work with my truck. I am pretty anal about things like that and they were very accomadating. I even needed my tunes by Thursday morning after ordering Monday morning, and received them at 11:45pm Tuesday night, so I was very impressed there.
All in all, it sounds like you need to talk with your tune writer, I know Matt called to discuss things with me before they wrote their tunes, ensure I knew what I was getting and what my options were. Then he even let me know if there was anything I wanted changed after getting my tunes to let him know and they would take care of it.
Granted I am not studded so I am only running their Street tune right now, I have the option to step up to Hot Street before studs too. Once I hit their Race tune, they recommended studs and let me know that straight up. They didn't try to upsell me to the Race tune package or anything. Just sold me exactly what we agreed upon, and got it done in a timely manor.
But since you spent the coin already I would contact your tune writer and see if they will help you out. I know Gearhead would, so I would think other tune writers would too.