Seems you are facing an incompatibility problem between the board and the expansion card. As you already have the latest BIOS I will suggest to the Give it a try with the latest chipset driver: Chipset: Intel® Chipset Device Software for Intel® Desktop Boards
Hopefully this will help you out on this matter.
We are having the same problem with Linux server.
In the bios "Configuration", "PCI/PCIe Add-In Slot" the main board give that "Slot7 PCIe x16" is "Not populated"...."
do you have a solution for it?
As a matter of fact this might be a compatibility problem due to the fact that most of these devices are tested and certified for server platforms, not desktop computers.
You may troubleshoot the issue testing another card (a regular one, as a wireless LAN card, a simple video card, etc.) to check that the port itself is working fine. Update the BIOS of the system you are using and in the other hand update the firmware of the card that you are having issues with.
Furthermore, check with the card manufacturer to see if the card has known compatibility issues with this motherboard or if this would be certified/qualified to work in this system.