I ended up figuring it out. It was a red herring for me in the device manager and what was actually happening was the Thunderbolt driver being pushed by Armory Crate is actually out of date/not current. Somehow it was popping up whenever I would put ...

Were you able to figure this out? I have the exact board and I'm attempting to install an expansion card in the PCIEX16(G4) and the same deal. It's almost like the slot is disabled by default but I cannot find any settings that explicitly say it is.