I am assuming you are watching the air cuts and you are sure that there is no mechanical operation of limit switches.
While spindles are usually the predominant noise source, stepper motors do contribute as well.
Turn off all limit switches, $xsn = $xsm = 0, once you are sure gcode will stay in bounds. If air cut fails (SpnDir flash) with switches turned off, then we are chasing wrong issue.
Maybe post a picture of you wiring/cabling
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This reply was modified 5 years, 7 months ago by cmcgrath5035.