Question
I have a Toro Ecxtra controller with a 1 hp pump and pump start relay installed. The problem is I get some sort of over-voltage or something on the MV/Pump circuit that deactivates the system.   The problem is intermittent. The cycle will start and run 1, 2, 3 times as programmed and then decide to malfunction.  I believe the problem might be with the COM connection within the controller. I've ran a brand new wire directly from the controller to the start relay to eliminate a problem with the buried wire, same result.
Yesterday I switched zones 1 & 2 wires to see if its being caused by the zone 1 valve hanging.
I'm out of ideas and am looking for any diagnostic suggestions.  Thanks.

Answer
Sorry for the delay of answering your question.
The problem is probably with the pump start relay. When a relay get a little age on it, they tend to draw a bit more power. This would cause the intermittent "fault" the controller is sensing.
I'd suggest a new pump start relay or you can use and intermediate relay to turn on the pump relay. This is done by wiring a small control relay to the pump start circuit of your controller. It then sends power to the pump start relay. By doing this you are isolating the controller from the heavy drawing pump start relay.
If you need further instruction for this let me know.

Matt