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Two things then. And bear with me as I am making some assumptions here.

  1. Imagine your bed gantry is not even and one side pulls down a bit. When you turn the rod - with the motors on - you turn the rod and get level again, while even the idle current applied to the motor holds the whole thing stable - despite the pressure from one side of the gantry pushing downwards. Then, when you disable motors via the code in S3D - the rod should be much easier to move and the force of the side of the bed pushes down hard enough to make a difference.
  2. Are all your stepper ports used up? If not, why not use Duet in all it's awesomeness and put one motor on Z, the other on a free port (like E1 for example) and then use true bed leveling, where the duet will probe near both screws and then automatically adjust the offset to make the bed even. :)