One consideration is the machine can only hold full and 1/8th step positions — the variation might be caused by how closely the metal rod and its spring are aligning with the nearest position — it is possible that at certain temperatures this is more/less repeatable.
The numbers you’re getting exactly match the specified mechanical resolution:
Mechanical Resolution .0005 in
(from: https://carbide3d.com/nomad/specs/ )
and are better than the expected repeatability/accuracy