That was part of the problem. I think I’ve isolated the issue. the machine believes it can move the z axis up quicker than it actually can leading to a deeper next cut after each lift. I’ve discovered that if the machine is asking a stepper motor to move quicker than it can the motor makes its normal move sound followed by a short series of moves instead of one continues move.
I have set repieter host to use the proper z axis move rate (100mm/m) but that doesnt appear to have an effect once I run g code. I did a find a replace (on the g code) and changed the feed rate for returning to the clearance plane. This lead to a mostly successful run, and totally eliminated my z axis problems
I am currently editing the marlin firmware to set a lower max on the z axis rate. I’ll report back if that fixes things