I am not using the 3-way SLI connector. I am using the 2-way flexible SLi connector.
I am using PCIE slots 1 and 3 as they are the x16 ones I believe.

Maybe it isn't a SLi issues, when I load BIOS F12e the second graphics card isn't even seen by the OS. Flashing back to BIOS F12d and SLi works again.