Just to update anyone interested:
Roy has tested the boards and says they are fine. He is making some more on Monday and will send me a new motherboard, but if the old one was OK I'm not very hopeful that will help. I did find a thread on here from routercnc in 2010 where he had some problems with a system3 setup that he traced to the power supply. Apparently that was missed steps rather than unrequested moves so may not be related.
Anyway I have asked Roy if he will send a new PSU when he returns the card as it seems to be the only bit that hasn't been swapped/eliminated.
Fingers crossed!