Actually I said that it wouldn't be related to the allocator because the legacy VGA ranges are not aren't allocated there.  This is the place to start to look for that:

Setting up VGA for PCI: 07:00.0
Setting PCI_BRIDGE_CTL_VGA for bridge PCI: 03:04.0
Setting PCI_BRIDGE_CTL_VGA for bridge PCI: 02:00.0
Setting PCI_BRIDGE_CTL_VGA for bridge PCI: 00:03.0
Setting PCI_BRIDGE_CTL_VGA for bridge PCI_DOMAIN: 0000
Setting PCI_BRIDGE_CTL_VGA for bridge Root Device
Allocating resources...

1. Make sure that that's the path to your graphics card.
2. Make sure that the correct bits get set in each device so that the I/O to the graphics card gets there.
  - The PCI_BRIDGE_CTL_VGA bit is in the device structure, so it doesn't affect hardware
  - Many bridges need some bit set to decode those ranges

I guess I don't know how to tell where the I/O gets stopped.  If 2:00.0 is misconfigured, but 00:03.0 and 3:04.0 are correctly configured, how would you know?  Most of the ways I can think of to debug that are all or nothing.

I've used PCIe graphics cards with my Tyan boards, and they are initialized correctly.  I agree with Kevin that a third card will likely have the same problems you're seeing.

Good luck,
Myles