Not sure I understand what it does, but it was ticked and had the UM definitions correctly in there!
Machine has printed from these settings perfectly before so I can't see what should suddenly get it to drive the zstage into the base of the printer!
It's because you turned of the "Update machine definition using settings below" in the advanced settings under G-Code. You really should leave that enabled in S3D, unless you want to grind more teeth
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