Are all PCIe slots are functioning at full link rate? Could be a PCIe lane. 72 of those pins are used for 36 PCIe lanes.
Maybe you got lucky and it’s a redundant ground or 12 volt pin, but I always assumed the pair of big 4-pin connectors were 12v and ground.
Could be also one of your DMI links to the ICH10 southbridge. It’s basically a PCIe x4 link, and will in fact work at x2.