When I change my Clearance Distance defaults, why don't they don’t get saved to the program?

When you create a new part program, the settings in Extras/Settings/Measurement are applied immediately and are permanent default settings. If you need different settings for a new program, then open Extras/Settings/Measurement from an empty Calypso desk or from an existing program. Make the desired changes to Retract Distance and/or Clearance Distance. Close Extras/Settings/Measurement then create new part program.