Hi Jonny,
Just my opinion…
Anything that reduces electrical noise and produces cleaner signals has to be good.
As you only seem to be having problems on the Z retract I would suggest that you reduce the Velocity and Acceleration on this axis until you find a 100% reliable setting.
(Just as an example my 100% reliable X and Y rapids are 4500mm/min @ 450mm/sec/sec whereas my Z rapids are only 1000mm/min @ 100mm/sec/sec – quite a large difference 1 : 4.5).
I don’t think you should ever assume that the issue is not of a mechanical nature, always consider all possibilities.

Tweakie.