In this case, I would check the logs of the system to see what is being recorded that would trigger the fans to run at full speed.
I would suggest running the latest firmware package (see update requirements first), and select “Other Chassis” and answer with a “No” when it asks for the system fans and answer yes for the processor fan.
Some setup is clearly off. Most of the Intel server boards have hardware control capability. All the fan speed and temp control is done by a chip, like BMC.
At cold bootup, the fans will be running at max speeds. Then the BMC controller takes over and the fan speeds would drop. Clearly the BMC controller is not working properly. The BMC BIOS may be corrupted.
On the server, there may be a jumper to recover BMC BIOS. I'd try to flash all the BIOS first, before try to recover the BIOS. The complete BIOS update can have 3-5 components.
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