If so,then you are right,its mostly because of the onboard card.
Try disabling it from Device manager in windows,if it didn't help,try this solutionhttp://www.overclock.net/nvidia/786979-pci-e-video-cards-not-detected.html
"Try putting one 9800GT first and choose PCI in bios.
If it works just restart the pc and change it to PCI-E.
I tried that and it worked for me, must be a motherboard bug."