I might be off base here, but with my AGP boards, I've had the option of choosing the video, whether it be AGP or PCI. Do you have that option with PCI-E verse PCI. Maybe you just need to plug the PCI-E card in, go into the bios, switch the primary video to PCI, shut down, swap the video cards and reboot.
Nevermind...looks like you already did that.
Nevermind...looks like you already did that.