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Ok, then i probably do not understand homing.
This is a cartesian gantry with XXYZ. The two joints for X cannot move separately. So my thinking was homing should be done for the axis instead of the joints; with only one homing switch for both joints (the axis).

Any shortcomings you need a hand working through?

havenofish , That is mm. It happens on Y and Z. I'm not playing with the Xx gantry axis at this point.

Darium, It is within the amplifier as far as I can see. LinuxCNC is sending the correct target position, and the machine is actually where it says it is, but it MAINTAINS a random (small) offset I can jog it around with the pendant and the offset stays the same. I can manually force the servo back and forth a bit, and it returns to the same incorrect position.

Upload pictures of wiring here on the forum so we can have a look.

You have tandem joints/axis so only after homing it will show axis.