"CMOS Settings Wrong" after Linux shutdown

I have a pile(18) of computers from a hospital that I am setting up for LinuxCNC. Fast enough for LinuxCNC with 15" touchscreen and rugged keyboard with a pole mount and good cable management.

Everything went relatively smooth except for a "CMOS Settings Wrong" problem that only occurs after I use the Linux shutdown (menu or "sudo shutdown now"). If I restart or unplug power from the computer without shutting down, everything is ok. But if I use shutdown, it won't boot until I clear CMOS.

Motherboards are Supermicro C7SIMQ and the bios was password protected. I cleared CMOS, downloaded and flashed the latest firmware and Management Engine from Supermicro. Cleared CMOS again and set up default CMOS. I started with the LinuxCNC 2.8 iso, updated to 2.8.1 and installed a few evdev and xinput packages to get the touchscreen working.

I installed new CMOS battery which didn't help. It's something related to the shutdown.

Any help would be appreciated. My work around right now is to either restart and disconnect power while it's restarting or leave it constantly on.

Added info - These computers included a battery backed up power supply, The backup batteries have been removed and the power supply works normally when plugged in. The power supply has two pins to short to start up the power supply after you plug it in. The only connection between the power supply and motherboard are the normal power connectors. So I expect the CMOS setting to be powered by the CR2032 when the power supply is unplugged. (And indeed it is) But if I perform the Linux shutdown even leaving the supply plugged in, the boot will fail until I clear and reset the CMOS.

Additional info - Problem also occurs running live with .iso with shutdown.
CMOS problem occurs with shutdown (and maybe suspend). Restart and Hibernate work as expected.

The problem occurs with the standard Debian LinuxCNC 2.8.0 iso. Same problem (won't reboot after a shutdown) occurs with the Mint 19.3 iso (no linuxcnc installed).

I think this is looking like an Intel Management Engine problem. I got a pile of medical PCs with SuperMicro C7SIMQ motherboards Corei3 that were locked with bios admin passwords. I flashed latest bios which also erased and updated the ME.

If I go through a shutdown, power supply comes up but the screen is blank. If I clear the CMOS using jumper pads and load default bios settings it will work until I do another shutdown. If I unplug power or hibernate, it works as expected.

I was hoping to set up a bunch of these computers for non-expert linuxCNC users, but this is one of those hair pulling snags that scares away non-computer types.

Looking into the whole IMEI fiasco, I came across the me_cleaner solution. I already had the bios file for the update, so I just ran me_cleaner to create a modified bios/me update with the AltMeDisable bit set.

C:\Users\JJT\Documents\me_cleaner>python me_cleaner.py -c h:\downloads\C7SIMQ7_602\C7SIMQ7.me
Full image detected
Found FPT header at 0x11010
Found 1 partition(s)
Found FTPR header: FTPR partition spans from 0xf2000 to 0x1b2000
ME/TXE firmware version 6.2.61.3535 (generation 2)
Public key match: Intel ME, firmware versions 6.x.x.x
The AltMeDisable bit is SET
Checking the FTPR RSA signature... VALID

I flashed this into the motherboard (using the SuperMicro provided ami.bat) but I still can't boot after a shutdown (until I clear CMOS).

Ok, I'm an idiot.
Dang computers do exactly what you program them to do!
These computers' power supplies are designed as battery backup and the BIOS setting for AC restore action just needed to be set to ON. (Untold wasted hours going down the wrong rabbit holes.)