When mutiple valves don't work all of a sudden the first thing I look for is a disconnected ground wire. You say there's two boxes. Is there 1 valve in 1 box and 3 valves in the other? Check at the controller. Is there two ground wires? One may have come loose. On occasion someone's shut the water off to the valves. Good luck!
If I can't fix it, it's broken!