As I have briefly mentioned in my MD5 chosen-prefix collisions slide about hardware implementation details, some motherboards require pins A1 and B17 to be shorted for an x16 card to work in an x1 connector. Let me explain why. The PCI Express Card Electromechanical Specification describes five "presence detect" pins:
A1: PRSNT1# Hot-plug presence detect
B17: PRSNT2# Hot-plug presence detect (for x1 cards)
B31: PRSNT2# Hot-plug presence detect (for x4 cards)
B48: PRSNT2# Hot-plug presence detect (for x8 cards)
B81: PRSNT2# Hot-plug presence detect (for x16 cards)
The motherboard connects PRSNT1# to ground. PCIe cards must have an electrical trace connecting PRSNT1# to the corresponding PRSNT2# pin depending on their link width. The motherboard detects if a card is present if it detects ground on one of the PRSNT2# pins. It is unclear to me whether this presence detection mechanism is supposed to be used only in the context of hot-plugging (yes, PCIe supports hot-plugging), or to detect the presence of cards in general (eg. during POST). One thing I have experimentally verified is that some, not all, motherboards use this mechanism to detect the presence of cards during POST. Down-plugging an x16 card in an x1 connector on these motherboards results in a system that does not boot or does not detect the card. The solution is to simply short pins A1 and B17 to do exactly what a real x1 card does