Hi Ushan,

I would reconfigure the system to makes sense to you. I believe zone three may have a disconnected wire or bad solenoid. I would trace each wire(should have different colored wires for each valve. The solenoids have black wires either one can be connected to the colored wire for that valve station terminal in the controller, the other black solenoid wire can be connected to the common white wire that goes to your common terminal in your controller. Also use water-proof twist connectors that have a gel inside the twist-on connector to help keep moisture away from the connection points. I would just rewire or reconnect all the valves and controller.
Apparently you have enough pressure and flow to run three (1 and 2&3) zones at once. You only need 2 terminal connections unless you need to separate zone 2&4. Simplify and give each valve only one connection to the controller. Aloha.

ushan, if you can turn on zones 2 and 4 together, manually, using either valve, then it seems that that you have a cross connection in the piping of these two zones.

I finally had an irrigation expert come in and even he could not figure out how we had 4 zones working with just 3 valves. He just went ahead and reconfigured the system by adding a fourth valve to manage the "extra" zone.
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Thanks all!
Usha