Maybe you should try a tunable ECU. As others have said, some chips will disable A/C when you plug it in, or even while you drive. I have the Apex'i power fc on my car, which lets you tune a wide variety of settings, and my A/C is fine at all rpms and speeds.

You mentioned 2 same Skunk2 chips operate differently on your car. This is kind of weird...are they like that as soon as you plug them in? or after a while, when the ECU adjusts to your car's settings?