There is a known issue between PCI-E 2.0 cards and some first-generation PCI Express chipsets, primarily VIA. The solution is simple enough, a modification to the VGA BIOS that allows the card to boot (initialize) in PCI-E 1.x mode.
NVIDIA was foremost affected because it was first to ship PCI-E 2.0. By the time ATI's first PCI-E 2.0 boards shipped, this issue was already coming to light, allowing ATI to implement the change from the start. Unfortunately, a few ATI and NVIDIA partners are somehow managing to still ship boards with the incompatible VGA BIOS. A few manufacturers are supplying affected users with an updated VGA BIOS upon request to flash their cards.