I would like to say Thank You to JAZZCNC for his help, the test programme showed a problem, with some odd noises and the Z crashing into the limit switch.
A really BIG thank you to Mike (Doddy) who after chatting with and suggesting to swap the leads at the back of the control unit so X was operating the Z axis the problem was cured, however not satisfied with just leaving it at that after several texts he advised me to set the step pulse and Dir pulse to 5, they were set at 1 also to slow the acceleration as it was a tad too fast, all this in the motor tuning within Mach 3, I swapped the Z and X leads back to where they should be and did several tests using my Vernier to measure the start and finish positions of the Z axis, which was good.
Today I did a job that took approximately 1.5 hours and it was perfect, so it looks as if the problem has been solved.
All I need to sort out now is a strange sort of squeaking noise on the X axis as it travels along, just started during the job I have just completed. it has always been lubricated at regular intervals with a silicone lubricating spray, (not WD40)