I completed a Hack using a 3TB UEFI Windows 7 boot drive and a 500GB UEFI Mac OS X 10.8.4 boot drive about 5 weeks ago. I use Clover as the boot loader to have access to both UEFI drives. Clover is installed in the EFI partition of the Mac OS drive. Lately, sometimes after shutting down the Mac OS and rebooting, The Windows option is there, but the Mountain Lion icon is gone. I checked the Mac OS hard drive and can see that the Mac HFS partition is there. As a last resort, I restored the drive using Clonezilla and thought all was well until the ML icon went away again. I turned off automatic system updates to see if that was the issue, but eventually the ML icon disappeared again. I tried booting with a Clover USB flash, and the ML icon is still missing.
Are there any software updates that could cause the Mac OS to become unbootable?
Any other ideas of what may be the problem?