Could you look up the BIOS and LSI firmware versions for your hardware?
I agree that it should work, there is no reason for it not to, but I've had this issue since Day 1 of this system (been running with the HBA in PCH slot for a year now because PCI x4 is enough for now, but decided to take another look at the system and try to resolve the issue)
The CPU also supports up to 16 lanes (Intel Celeron G4920), so it should be working, but yet it doesn't
EDIT: could the be a faulty motherboard, maybe?