Cutting through wasteboard

My X Carve is cutting too deep and is cutting through my waste board. Also when it gets to the end of the cut and starts to reverse it is not following the original cut. I dont know what to do and was hoping someone could offer some help!
Any suggestions?

When you ran setup, did you select ACME screw or the M8 or whatever?
Make sure you select the correct one. It will affect the Z travel.