I had that problem last month. It was caused by som tiny clog in one valve (membrane). It was solved cleaning the valve that keeps opening when other valves open. I hope it helps.

I imagine you have checked the connections of your controller, and made sure the valve works properly...

Water pipes do not go randomly. I would try to dig near the valve box to find the direction of the pipe under suspect, and perhaps locate the first sprinkler... And so on...