PCIe SATA III RAID controller card Linux setup
Solution 1:
We finally did end up figuring out the problem, it was the wrong type of cable.
We were using a forward breakout cable.
This particular setup requires a Discrete to SFF-8087 (Reverse breakout) cable.
Unraid.net has an explanation of the difference between forward and reverse breakout SFF-8087 cables, even though from the outside they look identical.