Wrong Os?

I have a friend with a ls swapped jeep. When I started tuning it, the iac wouldn't work. It was stuck at 310 in the scanner, with no control by the vcm tools. We replaced the iac, and check wiring...with no help. So we thought maybe something was wrong with pcm, so he had a new one sent to us. The first pcm is out of a 2002 avalanche, the new one was a 2002 v6 express van. Now it wouldn't crank with the v6 calibration, but the iac started working with the key on. I flashed his file into it, back to original issue. This car is wired according to a 2002 fbody automatic with a 4l80. Are we running into a OS issue?