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I have a dual stepper Z axis setup on a Hypercube driven by a Duet Ethernet board. The only problem I have with it is after finishing a print, I have a script in Simplifiy3D that lowers the build platform and homes the X and Y axes. Every time it does this, if I home the Z axis, the right side is a few mm higher and the build plate hits the extruder nozzle when it raises to the home position. I can manually turn the actuator rod a few steps and lower that side back to the correct position, but I can't understand why it does this. The platform isn't binding as I have taken it loose from the follower nuts and it slides up and down the entire range of travel freely.
Now if it use the Panel Duet and manually move the platform up and down, even over the full 300mm range, it never gets out of alignment.

Any ideas what might be going on?