here is a suggestion.
your car may absolutely hate this and piss itself, but it's worth a shot.
do a full write with the stock file. {put the stock file back in the car} shut it off for 10-20 seconds after the write. fire it up and try to get it to idle for about 5-10 seconds. just enough time for the ecm to check all the sensors and crap. shut the car off. it works as a hard reset. load the file you're currently working with in the car as a write entire. fire up car and go see what it does after this.
instructions per GM r&d engineering friend. seemed to help out a lot on my truck with this issue and other issues i was fighting. think of it more of a refresh of the ecm than anything else.
as far as i know hpt is only system that doesn't shut down the ecm on a flash, but the write entire does.