I have been running a pci graphics card on this system without issue.
My friend just gave me an agp graphics card to use, as well as a motherboard(same model board, faster processor).
After switching out to the new board and booting successfully, I used drivesweeper to remove the old drivers and put in the new card. I went into the bios to change the graphics from pci to onboard/agp. I get display until windows starts to load, then it blue screens briefly and reboots. I have tried starting in safe mode and the same thing happens, as the drivers load it blue screens and reboots.
I tried this a little while back with another agp card on the old motherboard with the same result. I thought the agp slot was bad, but I have just switched out the motherboard so it can't be that. He was just using the board and card in his old system without issue.
Maybe try this. Re-install temporarily the PCI card, boot into BIOS Setup and get that set so it runs, then proceed into Windows. Within Windows Device Manager, delete ALL the drivers for video cards and Remove the video card device, then shut down. Now install the AGP card, boot into BIOS Setup and set that card as the device to use. Save and Exit to boot into Windows. It should just boot with its own very basic VGA video drivers. Once in Windows, install the proper drivers for that card.
You MIGHT also have to Remove and then re-install the drivers for your Monitor, since Windows appears to recognize an association between the monitor and the card that drives it.