That motherboard (or rather its CPU) only has 16 PCIe lanes fed off the processor that are split between those two x16 PCIe slots. When the second x16 is not populated, all 16 lanes go to the first slot (presumably with your graphics card). When you plug the 1429 into the second slot, it should cause the fist slot to drop to a x8 electrically so that there are free lanes for that second slot. It is possible that either your graphics card or the motherboard's BIOS is not handling this case properly. You could try seeing if there are any BIOS updates available for the motherboard or an update for your graphics card.
Eric
