Onboard VGA interfering with PCI-E x16 slot?

Okay, so my computer died a few days ago. I tested it all, decided the mobo was dead. Replaced the mobo, but my gfx card was at the shop I tested it at, so I used another to run it for the night. Next day I got my 9800 gtx+ and put it back into my machine and it's a no go and I'd assume that since the other card was working in it that my 9800 is dead just like the mobo was. However, I see signs that also make me believe that the on-board video on the motherboard is preventing the 9800 from starting. Upon powering up the fan spins a notch, as if beginning to start and then being told "No." Also, if I turn my monitor off and back on while it's plugged into the card the card will full charge up and run it's fan at full speed, so it is obviously capable of doing so, it's just not be allowed in my eyes. It is a Biostar g31d-m7 motherboard and 2.61 AMI bois... I tried looking through the settings myself to try and disable the on-board, but no matter what I do and what I turn off I can always use it, and my 9800 won't work. Anyone help me?