Small update to this one... Its now semi solved.

I realised a few days back that my original attempt at bridging out the estop circuit was a bit flawed. I was using the LEDs on the controller board as an indication of whether the signals were active or not. When I first tried I assumed that the estop would get its power from the machine, but it doesn't. Its powered by usb, unlike the homing and limit switches which are on a 24v power source. The result being that when I bridged, turned on the power at the machine, saw LEDs for the homing / limits but not for the estop I assumed this was still this random estop problem, but it wasn't... it was the fact that I didn't have the usb plugged in.

I got sent a wiring diagram and realised the mistake... Bridged out the circuit and plugged in and have been milling parts the last few days. It has however STILL estopped on me mid cut, which is a little worrying as there is only a tiny bit of cable bridging the circuit. But just the once and I was able to immediately reset and continue.

I wouldn't say its solved by any means... For one I have no estop now. I'm dubious that the control card is paying attention to Mach's setting for debounce... I'll have a think / seek advice about trying to rewire to use the 24v power source for the estop and / or add a small capacitor onto the estop circuit to do a bit of debounce the physical way. All things which I'm aware you mentioned ages ago JAZZ .

Thanks for your help everyone!