edowney:
In material setup rapid Z clearance (Z1) & Plunge (ZZ) along with the Home/Start Position x,y,z can all be set up in different locations depending on your part setup circumstances (at least this is in my case I have actually witnessed it in my own projects). I have changed Rapid Z Clearance to 3.0" & the Home Start Z to 0.8" for actual movement from cut location to cut location the spindle travels at 3.0" above part clearing any clamps, raised wood of model cutout, etc... and when CNC is finished the project the spindle will return to home/start traveling 3.0" above part/project then dives to 0.8" and stops! Scary that first time but it did and has always stopped at 0.8" from table top spoil board!
These settings I have found are all separate entities I have never in any of my situations seen these settings change unless I change them even on a re-calculation of tool paths and in my case I would not want them to change because they all have a significant duty to perform in my project layout. But I always do get a message/warning to re-calculate tool paths anytime I have made a change on any of these settings which I do straight away so as not to forget to do it.
Sharkcutup