You're also running multiple VMs
As we all know, something like Windows can take quite a while to shut itself down. Even an open dialog window will prevent the Windows from shutting off, which will lead to the OS having to forcibly kill off the tasks and then having an unclean shutdown flagged, regardless of whatever times you set.
Always set in VM Settings for the powerdown action to be hibernate and install the QEMU guest tools in the VM. Now when a poweroff gets issued, the VM will hibernate in a second or two instead of having to actually perform a shutdown.