The solution to your problem is quite simple. I have used this mobo recently and with an ATI/AMD GPU.
Best BIOS for O/C is 0608.
But for your problem wich I had too, you should consider these 3 things.
1)Mobo battery low voltage --- plausible.
2)SLI Bridge can cause issues if not properly seated.
3)Just update your BIOS to the latest 1406 --- I believe this is the solution.Look at the description!http://www.asus.com/Motherboards/P5NE_SLI/#support_Download_30
Hope that was helpful enough.