Yes.  I have a SATA cable powering the riser and a direct VGA 6 pin to the GPU.  Also all fans spin during bootup, but only 5 are detected when the OS comes around (SMOS).  Also I have 2 molexes going into the motherboard for additional PCIE powering.  I have also tried directly powering the riser with a 6 pin vga power cable.
 I see that at max I am only using around 580W.  

Do you think it could be the OS not detecting 1?  Would it be worth my trying to plug 1 card in directly to the motherboard?