CPU fan seemingly picking random fan RPM

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I apologize in advance for the long post, but I'm trying to figure this stuff out alone and I'm getting nowhere. Also, sorry for the 'noise' ratings, but I don't own any equipment to measure decibel.

I'm sure it's my ignorance, but I'm unable to read CPU fan rpm via any 3rd party utilities (AIDA64 and BurninTest Pro) or inside BIOS; however, I can view through IPMI View and IPMI web-interface. Also, I can't figure out how the system determines fan RPM and why it seems to change at random. Setting the Fan Mode via the web interface doesn't appear to do anything except kick the fan up to 3000 RPM on Full Speed or 1000 RPM on all other settings.

CPU - E3-1275v6 (retail HSF)
MB - Supermicro X11SSL-F

Loud - the noise that Foxconn fans hit on boot when they max out rpm.
Moderate - still audible from 1-2 rooms over, but not as audible as 'Loud', perhaps half of Loud.
Low - reached this only once. what I would consider audible in room, but not outside of room.
Quiet - what my i5-6500 is with retail HSF. I can barely hear it inside the case, even under load.

4pinCPU@Fan1, no case fans attached

Startup
Sometimes Moderate through BIOS, then Loud at Windows login prompt
Sometimes Moderate through BIOS and Windows
Sometimes Loud through BIOS, then Moderate at Windows login prompt
Sometimes Loud through BIOS and Windows

Idle
No change

100% load
No change

4pinCPU@Fan1, 3pinCaseFans@Fan2/3/4

Startup
Same as above

Idle
Same as above

100% load
Same as above

I didn't put this above, however ONE time the RPM of the CPU fan adjusted as thermals changed. It was Low (from startup thru login) until I started running AIDA64 stress test and it responded accordingly to adjust for CPU thermals. ALL other times it has seemed to pick random RPM's and just sat at those RPM's without adjusting.

Another note (perhaps relevant), randomly Windows informed me Wired#1 stopped working with this message: Windows has stopped this device because it has reported problems. (Code 43)

This is my first time building on a server-grade motherboard (building a little minecraft/ark gaming server for the fam and friends), so that aspect is new territory and I'm sure there is something/alot I'm missing. However, could I have a bad MB and/or CPU?
 
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Apologies, you're right, there is no freenas specific question. I'm going to be using ESXi and then loading different OS's for different roles. Initially it will be for a minecraft/ark server, but I'll be adding freenas and plex once I've figured out whether I'm going to attempt docker or stick with ESXi. If that precludes my posting here, I apologize. Please delete this thread at your discretion. Thank you for at least replying though :) Nothing worse than a thread with 0 replies.
 
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3 Pin fans are controlled by adjusting the voltage.
4 pin fans are controlled by Pulse Width Modulation, and are known as PWM fans.

The Supermicro boards are designed to control PWM fans, based on CPU temperature, if the fan speed thresholds are correct in IPMI, and depending on which fan mode is set in IPMI.

Get rid of the 3 pin fans, and replace them with 4 pin PWM fans.

Set the IPMI fan speed thresholds to be compatible with your fan make and model, using the info in this Resource (see the Discussion tab above the Resource text for the discussion thread on the subject). Then try the various IPMI fan speed settings.

Pay attention to hard drive temperatures, as there is not a good correlation between CPU temperature and hard drive temperaturs, so a system that sets fans speeds as a function of CPU temperature may not provide sufficient hard drive cooling if the drives are busy.

There are several scripts available that control hard drive fans as a function of hard drive temperatures. See the following:
 
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