Unable to shutdown/reboot properly sometimes

I have tried add fix shutdown flag in clover configuration. Seems not fix the issue.
Sometimes they reboot/shutdown very quickly, sometimes just not reboot/shutdown until I hit reset/power off button on the case, and sometimes they take very long time to reboot/shutdown(more than 1 min)
Any idea how to fix this annoying issue?

P8Z77-V LX, I5 3470, GT 660
El Capitan 10.11.6