I have the same problem but with different cards. Any combination of two cards from GTX 650, GTX 680 and GTX 760, with or without NVIDIA driver. Both cards are recognized, but it is random for every boot what monitors turn on or not.
X99-UD F10 bios
Asus GTX 680 2GB
Samsung 840Pro 256GB
Most of system works OK with UniBeast, MultiBeast and Clover. Have USB audio, so haven't tested motherboard audio.
Sleep does not work. Seems to go to sleep OK, but when waking up the machine reboots. All my other...
Great build! I have a similar build with same motherboard but i3 processor, sitting in a huge noisy case.. How is the noise and temperatures in your case? As it is only CPU fan I would guess it's pretty quiet? :thumbup: