I've finally got back in the office from xmas and managed to try this out again - I hooked two Apple Dual Link DVI's and a standard Apple Mini Display port to DVI - Initially I had the same issue but as Paul suggested (thanks Paul) changing the DisplayIndex in the control window sorts it out!!
So simple but I swear I lost some hair over this!
I've got some more active DVI adaptors in the post, just for piece of mind.
Thanks for the responses with this