Hi Guys, I've had a better day today. Taking time from work to sort the problems out.
Thanks Kris for your help, it helped my train of thought a lot.

The stepper breaking from steps in rapid move in only one part of the program turned out to be a problem with the Mach pulse engine driver.
As the fog of a bad day clears I remember that the computer crashed during a Mach session so it is possible it corrupted the driver.
After reloading the driver a couple of times it now works perfect.
Ugrading to the lastest software update caught me by suprise with the new enhancements. The problem with the toolpath displaying black material on a black screen turned out to be a setting in Config/Toolpath. The material color was set to red=0 green=0.1 blue=0.1. Setting them all to 1 sorted that problem.
I fiddled with the softlimits and got them to work as I never had them configured before. The limits work with Machine Coordinates as they should but had me confused when setting them looking at the screen which was displaying Program Coords. Duh...

As I've been jogging up and down, the whole system seems to be a lot smoother so I tweaked the rapid speed up a bit and no stepper break away.
I can now put my feet up for the rest of the day, work tomorrow

Thanks guys
Cheers