I've some a similar thing with my NAS on a Supermicro X10 (I think) on Linux. I have had all kinds of trouble getting quiet fans on this board under Linux. I think it's a mix of BIOS fan control and other things that I ended up sinking days into trying to solve. Right now my solution is flaky at best, but eventually the fans spin down after a reboot.
Supermicro could be so good for "prosumers" but I feel like they are bogged down by historic garbage. I had to pay (crack) something in the BIOS just to use a feature.