If you test the voltage beween the common and one of the stations when it is turned on, you should be getting something around 25 to 30 volts AC (not DC).
While I don't know for sure how the typical timer is set up, it is possible that everything works, but a fuse still be blown that simply limits the current for the common. (I.e. the fuse protects the output of the device, not the device circuitry).
The other thing to do is remove the rain sensor from the loop. If it has gone bad for some reason, the would also be a reason everything went bad at the same time. Most likely, the common from the controller goes to the rain sensor, then the rain sensor goes to the common wire for the valves. If so, then you can just sort circuit the wires across the rain sensor.
While wires are disconnected from the controller, you can also test the resistance between the common and one of the valves. You should get something around 20ish to 50ish ohms. If you get an open connection, then you know the common has some how broken or become disconnected.