Strangely related, I think I am getting that same noise too. I sent my MOBO in for new BIOS chips. When I got it back all of a sudden I get a noise that sounds like a whining/squeaky fan. My GPU fans don't ramp up though since they are on manual control.
It only happens with my GPUs start a 3D application. It never did that before I sent my MOBO in. I just turn the sound up...it makes it go away
Temps are fine, no crashing, no artifacts...I am compelled to figure out where it is coming from though now. The only thing that changed on my mobo were the BIOS chips. Makes no sense.