rebooting shuts down hard drives

When I use Windows to reboot my computer it shuts down my hard drives so when
my RAID controller looks for them it can't find them. This causes windows
not to load because no drives are found. I then have reboot again using
either CRTL+ALT+DELETE or hitting the reset button to get it to boot
normally. Windows should not be shutting down my hard drives on a reboot.
Is there any way to get this resolved. My RAID controller does not seem to
have a spin up wait setting so if it can't immediately find the drives it
misses them. It does power on the drives but misses them on a reboot because
of a no wait setting. I still don't think Windows should be shutting down my
drives on a reboot.

Using an MSI 580X motherboard with built in RAID 0.