Follow this :-

1. Home your machine.

2. On the program page click in the pink tool DRO and enter 1, press enter.

3. Click in the pink Dia DRO and enter zero, press enter.

4. Click in the pink H DRO and enter zero, press enter.

5. Click OFFSETS page.

6. Click Fixture 1 (G54) button under active work offset.

7. Move machine over material in X & Y.

8. Bring Z axis down until it just touches, use a feeler gauge or a bit of paper to feel it in.

9. On OFFSETS page click Zero Z.  This should now show Zero.

10. Home the machine.

11. Move over the material in X & Y, turn rapids right down.

12. In MDI page enter G00 G90 G49 Z5.  Check position is 5mm above material.

If you then try different Z heights and they are wrong your calibration is out or machine is loosing steps.

Problem fixed
Many thanks for the time you have spent sorting this out and the expert knowledge shared.