Yep, that fixed it.
There must be a couple of flaws in the worm or wheel. Adding tiny bit more backlash made all the difference. I also went back to PHD2's default settings.
I had a quick look at last night's subs and I don't think there's a bad one in there.
I love it when things go according to plan.
I've never used periodic error training - I'll have to try it. It may help even further.