You have covered most of the troubleshooting listed in our article “System Fan runs Too Fast or Too Loud”. I would recommend inspecting the installation of the side cover to make sure it is properly mounted. If it is, I would recommend recording the logs of your system using our Intel System Information Retrieval Utility to investigate what might be triggering the fan speed.
I was able to speak with a tech. at Intel today. He had me try an older firmware version. But that did not work. He told me the BMC should be replaced.
Since it is a brand new server, I was issued am RMA for a replacement.