Does the machine run otherwise? You can jog the single axis you have setup to test? Perhaps you need to edit the RefAllHome script to match your setup?? RefAllHome need the axes active and the default home script is likely calling for all 3, X/Y/Z, to move, but you don't have those active yet? Can you go to the diagnostics tab and REF just the axis you have setup? If so, the RefAllHome script won't run until you get more axes setup, it's probably trying to do Z first and you don't have a Z setup.
I'm just guessing here!!