I highly suspect the plumber. Try this. At the controller disconnect the number 3 wire. Now run number 3. If only 3 puts out power then the wires are messed up. If anything else comes on then it's the controller. The wiring could be messed up at the valves or where the guy dug.
I follow you line of reasoning but that is not necessarily true. I would be true if it is an electrical problem, but the problem may be that the system has sand or small lime stone, gravel etc in the lines that are not letting the control valves shut off properly. So when any zone is turned on that pressurizes the line any valve that is not closing properly will come on. I suspect that this is the problem.