Argh!!!
Thought I'd do the right thing, and connect up all the sheilding wires to ground, but it meant the spindle sensor started giving some very erratic readings (3 million rpm is just slightly high...)
So cut the sheilding wire, and things went back to being stable.
I'm just going to leave the ground wires of for now, as everything appears to work how it should with them off. I think the real issue is that with the current control box layout, the ground wires are having to run past the transformer, bridge rectifiers, and capacitors, and they're picking up interference from them. I could redo the control box, but I'm wanting to make parts, so I'll leave that for a future upgrade, as I'm not entirely happy with the current break out board (even though it's repaired, I'm not 100% convinced by it's reliability).

Just need to get a couple airline connectors now, and get the control cabinet screwed shut, so I can get the lathe turned around and the workshop rearranged for the other new toy.