Can someone please help? When I start a job I zero the tool on the top but when I run it sometimes the Z axis starts + a few millimetres missing the job but when I stop and rewind start again its ok, its as if its reading the Gcode wrong?

zero Z axis when the tool on the top on THE MATERIAL.
(or setup and use "auto zero tool probe").

You need to click on [REG. Toolpath], AFTER you zero X, Y and Z axes
BEFORE
you
click
[Cycle start]

That makes no difference

That makes no difference

In that case, there are many things to things to check in sequence order.
1. Mechanical - Check esp. motor to ball screw coupling. Is anything loose or broken. Are they well lubricated. Are shafts parallel?
2. Electrical - any dry joints or loose connection on the wiring from Break out board and drivers to the motors.  VERY COMMON!
3. is the ampereage and sub-step settings at the driver correct?
4. Mach3
4.1 Is pulse rate too high?
4.2 Is speed and acceleration set too high.
4.2 What is the step pulse and direction pulse too low. Try 15 and 15 to see if it makes any difference. Then decrease.
4.3 Have the z axis travel been calibrated?
4.4 Are there any entries in the tool table for radius and length compensation?
4.5 Are you using the Auto tool Zero probe to zero z axis?