Just finished the following build:
Silverstone Fortress FT02B
HD 6970 2GB
1TB Western Digital Caviar Green
120GB OCZ Vertex 3
Asus p8z68-v pro/gen3
8GB Corsair Vengeance 1600
Typically, it has an annoying problem. On booting to windows 7, every now and then the mouse and keyboard stop working for a very short period of time (a stutter), every few seconds, for a variable amount of time. Nothing particularly seems to trigger it. I am using a Razer Deathadder mouse (wired), as well as a wired keyboard.
Having updated all drivers/etc, it still occurs. It occurred from the moment windows 7 was installed - but doesn't seem to happen in safe mode. Also doesn't happen in the BIOS, nor in linux.
I have absolutely no idea what is happening - anyone got any ideas?
Is Windows churning you hard drive at that point? If so you should have a thing on the ASUS disk that came with the motherboard called Intel Rapid Storage Technology Driver. Install it and see if it helps.
The other thing is that the Green drives are a bit slower than most, and it is likely struggling to keep up with your fast hardware.