If you did not rule out faulty system wiring or short-circuited valve solenoids, before you decided the controller was the problem, then you have to back up and check the wiring with resistance measurements. It might even be that you have an intermittent short in a valve solenoid, that will test okay, but will heat up and short out when a zone is activated. The last is checked with reading AC current, which is beyond the capability of a lot of multimeters, so an alternative is to disconnect one valve wire, and try a manual cycle on the controller.
By the way, what make and model are the zone valves (you can bring back a photo)