I too have been using the deskcnc controllers for some time now and have had similar trouble with the software when using the estop terminal. In my machines, instead of going into an e-stop mode, the machine would start moving irratically.
I finally disconnected the estop and disabled to pin from the settings and have wired all the limit switches to power a solid state relay which then powers up the controller. Ideally, these switches are never hit, but if they are, the controller simply goes off and I can set things right then.
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