This is the PCI 32/33 5V slot, yes? It looks like that only shares a lane with the Rear I/O VGA port, according to the block diagram in the TPS at http://www.intel.com/support/motherboards/server/sb/CS-032382.htm
Are you using the onboard video, or an add-in video card?
Do any PCIe cards work?
Yes. its the 32bit/33MHz PCI slot.
I'm using onboard video and PCIe is working properly.
The onboard network devices are also ok(they have an interrupt assignment)
I checked the settings for the onboard video.
The PCI Interrupt is also INTA# and there is also no interrupt assigned!
Since the bridge does not generate an interrupt, BIOS should program this value to FFh as per the PCI bridge specification. This is not an issue if the video card works well.
if there is no interrupt assignment my pci cards will no work.
The irq value in the pci configuration space tells the driver what irq to use. If it is 0xff the card stays silent....