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Numerous problems with HVAC. Fan speeds don't always respond, temp control won't always respond, circulate button does not advance the fan speed, hot on one side and cold on the other. These problems are always fluctuating. Some times the controls respond and other times they don't. I assume the HVAC control module is failing. I cannot find any indication the the control mudule has any self diagnosis capabilities. I have already disconnected the HVAC fuse and waited more than 60 seconds to reconnect. No luck with that. Any ideas?
You will have to search using google for your issue but I remember seeing something very similar to this and it turned out to be a bad ground that can either be repaired or you can replace the entire assembly.
The way you describe the conditions as fluctuating seem to point at the control module as the root of the problem. The connectors could be loose and or not locked into the back of the control module. That is a starting point for sure. if those are OK, then possibly a cold solder joint in the control module circuit board. If you can take the module apart, you may be able to see what solder joint (s) are bad by discoloration. Without a proper scan tool to diagnose the system, it's trial and error at best.
I've replaced my control unit twice now. It sometimes blinks and is unresponsive. Other times it blinks and IS responsive. Other times it is just a blank screen. So many symptoms for the same thing - a garbage head unit.
The second replacement was just a few weeks ago and the service description was "shorted head unit" but I honestly don't know how they determined that. It's an easy replacement though you do have to remove the console bezel to get at the two screws holding the unit in.
From what I can tell the C5 and C6 seem to have issues with the controller and problems like this are common. Unfortunately, unless you are a good electrical engineering type, the C6 version does not appear to be user-fixable.