I was talking to my Dad, yesterday. He has his own project going on with his 2014 V6 Mustang. Has gotten a Bama tune, BBK Throttle Body, and Roush intake, so far. He did some dyno runs, the other day. He said they wanted him to flash it back to stock, for some baseline runs. He said when he did that, then flashed it back to his tune, the car ran like crap, at first, and gradually got better over the next couple weeks. I'm wondering if both our vehicles use the same learning logic, and that's been your issue this whole time. May have to give the tune a good while to take full effect?