Problem with my z axis

So i have updated my cardibe motion to the 618 to see if it would fix my problem but no it did not. I have had this problem since i have reserved the machine new out of the box.

My problem i start the machine it runs thought the X and the Y then it runs to the bit setter hits the bit setter runs the cycle and on my screen it shows z axis is at 1.295 high i measured the bit to the waste board and it is 3 inchs. i rerun the setup again XY good then run the bit setter now it tells me the bit is 3.882 and the bit is 3 inchs above the waste board. then i zeroed the bit at .875. I dry ran a program that was set at .750 depth so when the program finishes it should be .125 off the waste board and when it got down to the waste board it still had .375 to go untill it hit .875. So rezeroed the machine reprogrammed my dry run set at .750 deep same problem going way to deep.
I have the Shapeoko XXL with the BitSetter and the Z-Plus axis.

Did you configure the Z-axis as HDZ?

https://my.carbide3d.com/docs/shapeoko-setup/

I ran thought the setup 2 times and ended up setting my z to the plus-z that seem to fix my problem i will have to run some programs on it see what happens.

 Thanks 
  Bob Hastrich