I flashed the tune back to the original read with WhippleOS and then logged it with key on engine off and did not have issues with the accelerator position reverting to a max value of 30%, it would register 100% everytime with throttle and etc torque desired matching. The accel pedal sensor values match as well with 4v on PPS Volt 1 and 2v on PPS Volt 2 everytime when you are full on the accelerator pedal. I then added just the CustomOS to the tune for canbus based flexfuel and flashed it, and in the datalog after 60-90seconds the accel pedal goes from registering 100% to a max value of 30% and the throttle went to 26% and ETC Torque Desired 535nm while the PPS Volt 1 and 2 do not change. If you key cycle it and let the ecm reset then you get 100% throttle back for another 60-90seconds. I have attached the 2 tunes as well as the datalogs. I get know check engine light or wrench light on the dash when this happens either. Hoping another set of eyes on this can make sense of it.
Thanks
WhippleOS file no throttle issues.teclog
WhippleOS_CustomOSCANFlex throttle issues 30percent accel position.teclog
LL3A-SEMWS6-AFD_WhippleOS_Read_CustomOSCANFlex.tec
LL3A-SEMWS6-AFD_WhippleOS_Read.tec