Thanks for the help Stephen and Sylvia,
I tried both of your suggestions and also tried the card in different pcix slots and still the issue persisted. I have since swapped to a asus sabertooth board and this has resolved my issues. Also it resolved an issue where on the intel board I had no rpm fan speeds reported (using corsair AF & SP fans) I now have these being reported with the asus board.
Shame as I think the intel board had slightly smoother performance with sli enabled. So yes this does appear to be a faulty board. Thanks again for your help.