I'll have to take a closer look when I get back to the shop. I'm guessing they aren't, just your basic grey insulated computer type cable. I did do a capacitor upgrade to the encoders to knock out some noise.
I can run most any other code with no ESTOPs but it's without the A axis running. I also can disable any AXIS on the controller, did that and ran through the code fine with each one enabled and the other ones disabled. So maybe the addition of the 4th axis introduces just enough more noise to cause trouble. What is troubling is that it's not what I would call intermittent or unpredictable. It will fail in my code at EXACTLY the same place every time. That's why I'm thinking it's something other than noise. not sure . . . .