Hmm, I've never seen a problem like this before.
Seems to be a problem with the monitor accepting the resoloution and refresh rate the computer boots up on before running Windows with all your settings, etc...
If you go into BIOS whne its booting up. Should be the Del key.
Scan through until you find something about the Video boot device, and which to boot up first.
Try setting if its not already to where your video card is. For instance AGP.
Then save and exit, and try that