Thanks for all the effort you've put into this, Craig. I'll ponder it all but I'm leaning toward and simpler input solution. BTW, I have 4 axes, not three, not that that matters!!
My physical Estop button has two contacts, one to the PMDX-126 and one to the ClearPath power supply. I also have a latching relay on the power supply input, I press a momentary button to activate the power supply. I can start the PS either before or after Mach4 is running, doesn't matter. But if, like you say, the ClearPath's are "de-asserted" and Mach4 is started first, I can understand there might be an issue.
I won't have time in the very near future to get at this, but definitely will get to it. Reading your advice, I'm leaning toward the inputs/programming method and not trying to use the Gecko ERR/RST input/outputs.
Thanks again,
Tom