So since I posted, and after reading @dlang 's mention of the Z commands, I looked into changing the default Post Processing settings. I changed the “Safe Retract Height” from the default (G53 I believe) to Clearance Height, and haven’t had any more issues thus far (>15 cuts all unique .nc files). The .nc files also have a bit of a disclaimer about the change: (-Attention- Property Safe Retracts is set to Clearance Height. Ensure the clearance height will clear the part and or fixtures. Raise the Z-axis to a safe height before starting the program.) I don’t now if this is the answer, but it has worked for me so far.
