If this is a new controller, the battery should have been OK. All the controllers I am familiar with use a 9 volt battery to maintain the timer setting in case of a power failure. The transformer supplies the power the rest of the time. Was the fuse blown? That is a rare thing. Did you replace it with one the proper size? There could be other problems, but the most common one is loss of ground. That is the wire coming from the controller terminal marked "C". This is normally a white wire, but a DIY could have used another color. This wire runs to the first solenoid which is the electric device that operates the valve. It is then linked to each of the remaining solenoids, in your case the last one. This is done by connecting the wires with either a special wire nut that has waterproof goop inside, or just a standard wire nut that is then filled with silicone. From you description of the problem, I suspect the ground wire has lost continuity between the controller and the first solenoid. If it was after the first solenoid, the first one would work but not the second one. I have never seen need to test voltage in a controller. Check the ground wire.
I just check the ESP6 manual on line. It states the battery must be a rechargeable NiCad 9 volt. NOT Alkaline.