Most likely one of two reasons, first is the cutter getting pulled out of the collet with the cutting forces. Second is you are loosing steps on a Z+ rapid move and thus as it does not go up as far as Mach has instructed, and thinks it is, it will go lower on the next Z move down.
For the first option you will need to make sure the collet is tight enough, for the second you need to detune your motors a bit, ie reduce accel and/or velocity
Hood