Can onboard PCI/VGA and PCIE/VGA card coexist ?

Hi,
I am attempting to run Knoppix (Intel motherboard) with both the onboard VGA and a PCI-*EXPRESS* (PCIE) VGA card.

When I setup the BIOS to use the onboard VGA as the primary, the PCIE card does not "appear" on the PCI bus
(i.e. it's not listed in /proc/pci or the scanpci output).
And when I setup the BIOS to use the PCIE VGA as the primary, the onboard VGA does not appear
(though a 3rd PCI/VGA card *will* appear).

I.E. setting the onboard VGA as primary will make a PCIE VGA "disappear",
and setting a PCIE VGA as primary will make the onboard VGA disappear (but not a 3rd PCI/VGA).

Any theories at all would be greatly appreciated.
Thanks !