I read a similar problem with a 4L60-E with a Corvette that had been modified with new internal heavy duty parts, and a shift kit. the tech mentioned something about "Torque Management" program in the PCM that conflicts exactly opposite of what we are trying to do with a shift kit, fights it all the way, here is one post I found- good reading.....
http://forum.efilive.com/showthread....o-HD-Shift-Kit
http://forum.efilive.com/showthread....-and-shift-kit
http://forum.efilive.com/showthread....ift-kit/page2&
maybe this is the issue you are having? Have a good one!
Ben Smith