No idea how this works but as Tweakie has since come up with same conclusion on Mach3 support forum totally independent from my findings, it would appear to be the case it happens and is known.
My post
"having occasional problems, axis will refuse to operate in one direction, jogging a different axis then frees the original axis to move as required"
Tweakies response
"issues such as this can occur when using an opto-isolated BoB feeding into an opto-isolated driver"