Throttle only half way after segment swap.

[2500HD8.1]

I have a 2002 2500HD Silverado with an 8.1l and an Allison 5 speed transmission. I have converted to flex fuel by installing sensor and doing a segment swap with the 2002 Tahoe file that is recommended to use to activate the flex fuel portion. After the segment swap everything seems to be working except for my throttle. After doing the segment swap I copied everything, except the flex fuel portion, from my original tune back into the segment swapped tune. When truck is not moving the throttle follows pedal all the way to 100%, but if I am moving the throttle will only go to 56% even though the pedal shows 100%. I have also noticed that my shifts are now shifting later after the swap. My truck has the electronic throttle. Any suggestions on why this may be happening? I have also disconnected the battery for over 30 minutes to see if a hard reset may fix, no change.

Update - Forgot to say the only segment I swapped was the engine segment, should I have swapped any of the other segments also?

[2500HD8.1]

Finally figured it out, it was ETC TPS Max vs. RPM vs. % Max Available Torque setting under Torque Management. Set table to all 100s. I had tried changing this table before with the original segment and it caused erratic throttle surges when letting off throttle, so wasn't sure what would happen this time, but decided to try anyway and it seems to have fixed my issue.