SuperMicro Motherboard Does Not Show All Cores (FIXED)

Long story short; I had an UNRAID server that was only recognizing one of four processor cores.  After much searching / trial and error, I finally fixed it (just today) and thought the solution might be useful to others trying to increase the longevity of older systems.

Short solution:

Set JPME2 to 2-3 position before upgrading BIOS on SuperMicro X10SLH-F-O motherboard; then move back to 1-2 position and clear CMOS.

Failing to do so can cause issues with Intel Platform Server Services.

Long story / details:

System specs summary for easy searching:

SuperMicro X10SLH-F-O with latest bios (3.3a)

Intel Xeon E3-1276v3

32GB DDR3 1600 ECC (KVR16E11K4/32)

Boot from 32GB SanDisk Cruzer Fit

Various assortment of drives for JBOD storage

This system was originally running Windows Server 2012 and all cores were properly detected, so I started off assuming it was an UNRAID specific issue.  In the end, it is likely that a BIOS upgrade is what caused the issue; not an OS change.

I had tried UNRAID updates, BIOS updates, IPMI updates, confirming all cores were enabled in BIOS, disabling C-states and T-states in the BIOS; and I was actually writing this post in the form of a support request, but when I went to upload the diagnostic data, I stumbled into some interesting additional information in the hardware profile.

Interestingly; it showed that UNRAID detected a 4 core / 8 thread processor, but said only 1 core is enabled:

     <configuration>
      <setting id="cores" value="4" />
      <setting id="enabledcores" value="1" />
      <setting id="threads" value="8" />
     </configuration>

This lead me down a whole new trail of searches which eventually lead me to the following forum thread:

https://forum.netgate.com/topic/114231/solved-quad-core-only-showing-single-core-after-supermicro-bios-upgrade

Following the steps suggested by SuperMicro to update ME BIOS worked for me.

Try the following to update ME in BIOS.
a) Power down, set JPME2 jumper to pin 2-3, power up then flash BIOS. Please make sure the BIOS has been reinstalled completely.
b) Power down, set JPME2 jumper to pin 1-2 after flashing BIOS

Then, please kindly try to power down and clear CMOS to see if any changes.
For clear CMOS, please following the instructions below:
1.   Remove AC power
2.  Remove onboard CMOS battery and wait for 15~20 minutes
3.  Place the battery back in
4.  Connect the AC