I do need to hold my hands up here, Jazz - as Richard said - I did advise him to ask on the forum for specific help on Mach3 (in this case the configuration for shared limit/home switches - I think from reading the PDF that is all managed by Mach3 / Input configuration, but without a working installation to test that I'm flying blind).

Yeah, there's a lot of conversation behind the scene here which I did try to help catch up with the relevant bits on the forum with my post (and discard the obsolete/rabbit-hole info), simply, it's a lot of noise that would have run to many pages and with many threads. State of play time-now is I'm going to verify/test the board/opto-isolator config to demonstrate the current (it's changed) behaviour - if its behaviour is as Richard has measured (I trust only my eyes), then to condemn the BoB and replace; the reluctance to date is due to the physical build of the controller box - but to recover that we're talking of mounting a ribbon extender to a DB25 on the panel and relocating the BoB somewhere all together more accessible within the enclosure. And in doing so the BoB will be selected with the standard opto-isolated limit switch inputs, and then we'll all be back to a nice, known state, and Richard can hopefully move forwards with a working machine.