Did you double check it was on pin 42 on the blue Ecm connector, if it is maybe the tune did not go through, because if the a/c part works good, and the engine side doesn''t it has to be the blue wire signal, try splicing the blue wire to battery voltage, first unplug the blue connector from the ECU, when you do that both fans should turn on low...
Had a 99 GMC ESCB with LQ4 conversion and Nelson Performance tunning, currently workin on my 82 SCB GMC with carbed LQ4 conversion in progress, Also have a 00 SS Camaro that runs mid 11's all day long with bolt ons, Drag race my 79 malibu that has a 496 BBC runnin 10's on motor, shootin for 9's with the 250 shot of nitrous in its near future. Use my 04 2500 chevy to pull my rig around and drive the fam in our 07 NNBS yukon, Die Hard Chevy Fan Till The Death.