Next cold boot enter your BIOS first and see what it shows you.
If your motherboard supports multiple profiles you might want to check what the default profile's setting are. I still dont see why auto wouldn't pick it up every time although.
Are any other settings changing? Maybe set something manually then see if it goes back to auto after a cold boot. Could be a dead CMOS battery or somthing.
Post something in the motherboard forums, I can't think of any reason the video card would cause this.
So how do you like Asus's 460, I'm thinking of getting one.