Thanks Eddy, will have a read now.

I'm pretty sure I've narrowed the controller problem down to the BOB ( I knew having separate drivers would pay off :) ). Each axis works OK by itself when other are unplugged. And swapping the BOB outputs to different M542s moves the problem axes around.

I should take the long axis drive apart now and inspect, so that I can email the seller with all the bits I want replaced in one go.