I did toggle the active low, and it works. But after saving this setting, then exiting Mach3, next time I start mach3 the settings are still what I saved them at, but I have to disable the Estop again. Sometimes, when I get it to work properly, half way through a movement the Estop starts flashing again, and I have to disable it. So I leave it disabled now.
The micro switches seem to directly switch off the motors, but have no effect on Mach3. When the a given axis hits a switch, this cuts out that axis motor, but Mach3 thinks it is still moving. I'm not sure if this way is better than "Limit switches" or not so good ? or is it just not configured to Mach3 properly ?
I have tried the "Automated setup of inputs" tab in "Input Signals" but it finds neither External Estop switch or micro switches.