I posted here yesterday asking for help on a similar problem yesterday: GPU keeps working (fans spinning) for a few seconds after shutdown - Windows 10 Forums

Basically, what happens now is as follows: When I press shutdown from start menu and the PC screen goes black at the end of it, I can hear components stopping their work, but pretty much all fans keep working (PSU fan, case fans, GPU fans). They work for 20-30 seconds and then I hear a Mobo beep (the same one you hear when you turn on your PC) and the PC boots back like it's nothing. When I reach login screen and shut down again from there, the PC fans again keep spinning after components turn off, but only a few seconds this time. The PC components then turn on and immediately turn off together with the fans.

Sorry for the poor phrasing, English is not my native language and I try my best here.

This complicated double-take shut down process only began after I disabled fast startup in Windows 10 (some guys on various forums suggested that I do that). Before I disabled them, the problem was like the one I linked to in the beginning. The whole problem started after I installed a second HDD. During the installation I also removed the GPU to allow me to fix some cables.

Besides the shut down, the PC seems to be working just fine. No crashes, no BSODs - nothing. Only this strange shut down.

Things I've already tried:
  • Disabling fast startup
  • Removing my second hard drive
  • Changing its SATA plugs
  • Changing SATA cables
  • Changing HDD power connector cables
  • Removing and putting back the GPU
  • Updating chipset driver
  • Shutting down from login menu