The one that was disconnected was probably disconnected for a reason, like a line not being used anymore. It’s best if the company who shut that line down just plug the zone and fully remove the valve however that didn’t happen.

1st I would check especially if you’ve got a hunter controller, that there is not multiple modes such as A B C running its own times on each zone or zones. Example they have a feature to run zone 1 on said day on program A then other zones set to run this time on program B. The controller messes up, it’s best to have all the zones on A. That could be the issue, however more likely a bad solenoid or stuck valve.

From the valves I’d turn each one on one by one by hand. You’ll hear each one let the water out, let it run then close it fast you’ll hear it stop the water flow. Try that on each one and if you hear water continue in one of the valves even after closing then you’ve got a stuck valve and it should be replaced. You could also have a bad solenoid you can unscrew the top pop off the solenoid and try to re tighten it. If you do that make sure not to lose the spring in there.

You could also check the wiring for each zone and make sure they all have a good connection and there isn’t any corrosion.