I have a Asus motherboard P5Q-Deluxe with 3 PCIex16 slots. If put an XFX 5670 card in the secondary graphics card slot (with a non graphic card in the primary slot), the machine will not post. If I put it in the primary slot it posts fine. However I can put an nVidia 9600GT in ant slot, both primary and secondary slots and even the 3rd PCIex16 slot and the pc posts ?
I do need to have a non graphic card in the primary slot, so it seems that ATI cards are a non starter unless this is specific to the 5670 ?
You may have discovered a quirk with the way the gpu bios's negotiate with the motherboard, but are you losing any functionality because of this ? Have you tried running two video cards, with your nvidia in the first slot and ATI card in the second slot. Is it active then, only under WINDOWS 7, you can run two video card drivers for different brands, though I have not tried it.
Could be addressed in a motherboard firmware update. I know some motherboards specifically say the first graphics card needs to be installed in the primary PCI-E slot. It could be that for one reason or another one works and the other doesn't, but the manufacture may not support it period. I've seen some board that actually have a physical card that you can flip to allow a card to be installed in the 2nd slot. The little board changes the bus around.
Why can you put your other expansion card in the 2nd PCI-E slot?