Thanks for the thought process, JAZZ. Actually I feel the last line is probably the way it will end up going, and getting used to the idea sooner rather than later will likely save me a lot of grief. I can of course re-use many of the components - especially the electronics and motors - as they are likely not letting me down.

Just as a point of note, I am using the Parallel Port, but via my own design BOB. And before any alarm bells start to ring, I'm an electronics engineer by profession and did it all properly. AFAIK it is rock solid, and just to back up that rash assertion, my weird axis behaviour does not change if I swap the X & Y motor wires over. More specifically the axis behaviour remains unchanged, despite the X and Y drives and therefore BOB signalling and Mach3 paths are swapped.

And that's why I think your last line probably applies!

Cheers
Graeme