Are you rebooting from within the VM or from the FreeNAS GUI? If from the FreeNAS GUI as I suspect, this is expected. the only way to do a clean shutdown from OUTSIDE the VM is via ACPI. There is no proper reboot.
They could send SIGTERM, wait for the process to exit and start it again but this is not the same as a "reboot". The should have 5 buttons named as follows:
Power On - Normal start
ACPI Shutdown - SIGTERM
Power Off --force-poweroff
Power Cycle --force-reset
Restart - SIGTERM wait for process to exit, Normal start.