From AGP video card to PCI video card

Hi, I have a Compaq computer that is using an AGP video card. I wanted to replace it by a PCI video card. The computer is modular, and the PCI card buses are not on the motherboard, but on another part that is connected on the motherboard. When I add the PCI video card to that board, and reboot the computer, it’s beeping to tell me that no video card is present. When I put the AGP video card back on the motherboard, everything return to normal. I called Compaq, they don’t know what to do.
I hope that you can help me.
Thank you very much
Phil