When only one processor is installed, the second PCI riser slot on the motherboard is not functional. The motherboard does not see any cards added to the second PCI riser.
Additionally, some of the PCIe* slots on the first riser may also be non-functional.
The solution is to move the riser card to the upper slots, which processor #1 controls.
|This image was taken from the Intel® Server Board S2600WT Technical Product Specification, section 5.4.1 Riser Card Support, Page 38 as an example.
Alternatively, add a second processor to enable all the risers, slots, and PCIe lanes.