I have just had a thought.
Maybe it is assigning the GPU wrong.
In my case, this happens but thankfully it doesnt make any difference.
I'm not sure how it could be getting it wrong for you. But for me, no matter what oder I have my GFX cards in, my 560 Ti is seen as GPU0.
Maybe you need to force GPU1 rather than GPU0 and see if that makes a difference.
The other option would be to try the V7 Beta, it sets itself up like GPU Tracker does.