Thanks to Dean, the problem seems to be sorted - it was a software issue and required a reinstall of MACH3... but as of this evening I think I have a working machine. I have just cut a square that is square and a circle that is circular for the first time. It has only taken Lockdown to push me into getting it done! The calibration and squaring process is a bit of a pain but less painful than I thought it was going to be. Only slight hiccup was accidentally plunging a centre finder into the bed. Scary and funny in equal measure, how casually the z axis just kept pushing it into the MDF. Machines really don’t know or care. Reminded me of the bit at the beginning of the MACH3 manual:

“a computer is quite prepared to rotate an 8" unbalanced cast iron four-jaw chuck at 3000 rpm, to plunge a panel-fielding router cutter deep into a piece of oak, or to mill away the clamps holding your work to the table.”

Hopefully I can start using this mighty tool now, with no more nasty surprises! Thanks everyone for the help, it’s only taken the best part of a decade!!