More than likely the fan on time or the AC pressure is causing the fans to stay on. There were a few different pressure transducers used as well. The OEM trucks used a 500psi sensor where the older Fbody and C5's used a 450psi sensor. So the sensor scale programmed in the tune needs to match the hardware so the AC fan pressure settings function correctly.
Unfortunately the pressure transducer tables are not populated in HPTuners. I have a list of parameters that need to be added that I plan on sending in to them soon. AC functions will be part of those parameter lists.