If you wire this correctly, you have a "hot" wire,usually black, from each of the zone stations in the controller to a solenoid, and a single ground wire, usually white, from the Common or Ground terminal in the control box. The ground wire is linked from one solenoid to the other. My first guess on you problem is that this ground link is broken/not connected at one link and the ensuing solenoids are the ones not operating. These connections are made with special waterproof wire nuts. Hope this is you problem as I can't think of anything else that might be at fault.