What make and model?
I have an '08 dodge charger Daytona, and I had a similar thing happen...
The techs reset my tuner, and advised me to just skip the key cycle........ Just to hit the check mark to continue.
Worked for me.

I am no expert.........but I believe the shift timing is during wide open throttle.

Oh,......... This is also on a hot tune for the car.........

I drive a dodge car..........but if it is any help, I also adjusted my shift timing to a higher RPM, but under normal throttle, it shifts normally. Hope this helps.

Ok.........
After posting my above review of the intune...........I may now need to retract.
As a result of this new found power and enjoyment in driving, I have recently become the proud owner of 2...... That's TWO speeding tickets in ONE DAY! :shock:
So................. Be careful people!! This ...

Since I have not seen a forum for it, I will post up.
I received my new intune on Friday, and had a few issues with set up on my dodge.
Called tech support this morning, and in 10 minutes, I was off and running!
This is a FANTASTIC product, and in my humble opinion, worth every penny!
My Charger ...