For my dual monitor support, there is a separate section in the display options (configured thru the video card not the OS) where you can make all the adjustments needed instead of letting the OS decide.

I have had a similar problem on my wife's pc where the bios would load, windows screen would splash, and then when it was time to load windows, the monitor would go black and the orange light would blink. All the drivers were up to date, and everything else was in line. The fix ended up being hooking the monitor up with a dvi cable instead of vga. I can swap them back and forth now and don't get the problem anymore.

Sometimes its the most random thing.