Truck shifts like crap on tune...didnt before

[BLFX4K]

So at 30,000 miles I had my 30k service
Truck felt great, shifted awesome, mileage improved and I was happy

At 32,000 miles, after my highway trip to cali and back to Vegas problems began. The truck began shifting really hard and feels like its on the verge of failing, this happened after a program to level 3, was set to the appropriate timing as I was using 91 octane, not 93.

Yesterday, at 34,500 miles I replace the battery. Put in the new one and she cranked right up, on the stock tune, shifted blissfully, smooth and not a jerk or thud into gear.

Retuned the gryphon to level 2 and problems started again. Is there an update I'm missing or corrupt file in my tune that's causing this to where I should flash the programmer again? Have not updated since I got the programmer, back in July of this year.

Shift levels are at 0-0-0

Still shifts hard into gear unless I'm shifting at 1500 or less rpm and only does it on the canned tunes.

Any help would be great