I was thinking of exporting the config and do a clean setup from scratch in parallel to see if that fixes it.Maybe that could be an approach for you as well?
I had a similar problem a while ago on older versions.I fixed it by:System > Settings > MiscellaneousAnd then disable all of the periodic backups:Periodic RRD Backup > DISABLEDPeriodic DHCP Leases Backup > DISABLEDPeriodic NetFlow Backup > DISBALEDPeriodic Captive Portal Backup > DISABLEDReboot and the now shutdown and reboot worked great.