I have ran across 3 or 4 faulty Pro C's right out of the box. None of them had your symptom though. Also not for a few years. They may have fixed the problem. The obvious question is, did you install 2 three station modules or just one? It sounds like you only have 6 stations. Maybe you have one wire hooked up to the pump terminal thinking it's a zone.
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I just remembered something. I believe if you install a module while the controller is plugged in then it wont recognise it. Try unplugging the controller, take out the modules and reinstall them. I'd take the back up battery out also just in case. Good luck!
If I can't fix it, it's broken!
