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I had a look at the Zapp website and the documentation there doesn't mention the estop pin. However I then loaded up the .xml file provided and ran Mach3 with it and it is set to port 1 pin 10 active...

Sounds to me like you may be using the wrong Input number or not set the port number or something then because mach isn't seeing the pin state change.

If you had the correct pin number then...