i have searched and read through a ton of threads on this subject but haven't seen my exact issue. Our 1994 C4 that we are rebuilding has the C68 electronic controller that had the typical power loss and freeze-up of the controls on power head. I sent controller and programmer to Bryan at Batee.com and he confirmed they both had bad caps and he rebuilt them both. I re installed them in the car and all functions work flawlessly, except the command signal to compressor clutch is for the lack of terms, "inverted". All zones coincide with their buttons, but the compressor only turns on when you press OFF, Vent, etc.....everything that isn't supposed to have compressor function does, and vice versa. Defrost, max, auto has no compressor trigger. Has anyone else experienced this? Bryan has been great, sending schematics, and suggested maybe the PCM was the issue....however i have the original to the car and a new PCM and it is the same for both. I have the FSM as well, and have verified signal from programmer to PCM, but as stated, signal happens on the opposite buttons it should.
not sure what to do, i just can't see how anything except the programmer could cause this. maybe it has a diode or something back feeding? not sure how to test the communication between head and programmer.......

 

I can't help you with troubleshooting, but there may be a work-around to this problem. You could place a five pin relay (with N.O and N.C. contacts) to feed the compressor using the normally closed contacts of the relay to feed the comp. clutch. The signal from the C68 will power the coil of the relay. Sequence of operation is; when relay coil is energized the relay opens it's contacts and cuts power to the comp. clutch. When relay is de-energized the reverse will happen. (contacts close and powers Comp. clutch. ) A switched power source (hot with key on) will be needed to power compressor clutch. I have never tried this before, but in theory it should work. That's all I got!

 

that is a pretty good last-ditch option, thanks...way to think outside the box..
not sure it'd be successful