Did you shut off SLI in the video driver before pulling the second card out?
The video driver is smart enough to figure this out.
There may be an option in the bios to boot to a single video card as well, change it to one card if it is there.
There is no BIOS option, and there never was. The closest thing was a little card that you'd have to flip if you were using SLI. But even then, this only configured the PCI-Express lanes, and this was all fixed by PCI-Express 2.0 (which this board has).
Still, it wouldn't hurt to reset BIOS to factory default settings. And I've taken it you've tried both cards and both DVI ports?