Re: Z axis cutting deeper than expected
Ok this is a total guess as I have no experience with steppers (as I assume this machine is). My wild guess is maybe wire noise is send extra steps to the Z when either the x or y moves. you could likely test this out fairly easily and my guess its whatever had to move out to do the next part of the pocket. Should be able to do a line made up of segments and see if the depth of the cut drops on each segment.
Anyhow - just a thought.
In case anyone is wondering, I'm the twin of the other gfacer on cnczone...