I have this exact same problem and I contacted SM support (Europe).
This is what they said:
Hello,
This is to be expected in your configuration. Our mainboards are part of our buildingblock solutions. this means we have a list of supermicro chassis, that are validated for this mainboard (see list on the productpage). When using a 3th party chassis, then we see this issue often. because this is a serverboard, our chassis have fans that have a minimum RPM above 600rpm, and this is required. Our boards also have a lower tresshold, of 600 rpm. below this, the fan will be flagged as "failed". When a fan fails, all other fans will revv up to compensate. In your 3th party chassis, this means the "failed fan" will now be above the 600rpm tresshold again, and the fans will return to the set speed. this causes the fan to fall below the 600rpm again, and all fans will revv up again, and so on and so on..
The tresshold is hardcoded, and cannot be changed. Also a ipmi reset will not solve this. Only way to solve this is to use validated fans as in the validated chassis.
So, I'm guessing I'm SOL!
Cheers