@czar666
We use many pcEngines MOBOs and almost all have different sounds at shutdown and start-up.
According to our observations, the sound you hear usually depends on the amount of stopping and starting processes and resource requirements.
This small unit is not a power machine and it also depends on processes how long it takes for sound exactly what state you are restarting from.
The latest BIOS 4.12.0.1:
https://pcengines.github.io/#mr-35
It’s good to hear that you’ve achieved a reassuring result.
PS:
4.11.0.6 not recommended "stepping stone" in the BIOS life, for example we did not update to this release.
(4.11.0.4 similarly, can cause problems)