I have pinned down the culprit. It’s my spindle, or the powering of it anyway. A ran a job with a pen crudely attached to the spindle, chose a long one (27 hole array I have failed to make in wood ten times now) to try and give me the best chance of seeing my intermittent fault, and ran it with and without the spindle powered up.
So I’m guessing it’s something like the routing of the power cable (too close to the board?), possibly static (I’ve earthed everything except the spindle body), I’m really not sure. Anyway, I’m mighty relieved, I have a way forward. Thanks for your help all. I will hopefully stop turning proto-signs into definitive and bloody expensive firewood.