the ladder is written by the OEM, in this case Leadwell, so things can be set up and programmed for different machines.
What form does the EMG Overide take? is it a button you push in to overide overtravel's or?
Can you tell if it goes into an input or is it a hardwired function?
Did you record the mode switch pattern when it was working?
It almost sounds like you have a intermittent power issue on the 24vdc supply.
It makes no sense that the EMG overide should be tied into the function switch.