Generally there is a fuse, either eletronic or replaceable. If it was a fuse you wouldn't have power at the terminal block. Your description is a little confussing. You said "a single zone is setup to run, ALL the zones get power where they connect on the box". when you say all stations have power, are you measuring 24v at the terminal block? on all stations at the same time? If so, there is something wrong with the controller. A controller will never turn on all stations at the same time. do one station at a time. measure the voltage at the controller. go to the valve and place your hand on the solenoid (the solenoid associated with the station that's on). it should have a slight vibration. If not there is a disconnect somewhere in the system. I'd repeat this test for several different stations (in different valve boxes). If they all come up with no vibration, there is a very go chance that there is a cut wire. Also should mention that a common wire (generally white) is disconnected it will give the same symptoms (and it's a lot easier to fix). Good practice is to take voltage readings off the wire directly and NOT off the terminal block itself.

Call your installer, that should still be under warranty.

Have you done any work that may have affected the wiring? Could the common wire have become a station wire and now the entire system turns on when you try to turn one station on?