You must go into "advanced tune" and manually select everything "stock" -- shift points for each gear, shift torque, everything. That's how I used to run my winter setup with teh superchips. Just AFM off and even stock shift torque.
It takes a while via the embedded menus the first time or two, but then you get the hang of it and going into advanced mode becomes second nature. I don't think I ever tuned "quick tune" ever. Always "advanced".
Hope this helps...
--zepcom