Try clearing the CMOS then check the SATA setting. Switch to AHCI or IDE, depending on the situation.
After updating from Windows 8 to Windows 8.1 had the "SecureBoot isn't configured correctly" nag in the bottom right hand corner of the desktop. I updated the bios to the latest version after which it would not boot. I couldn't figure out what the problem was until I read "alexoiu" post switched SATA back to AHCI (which it was originally), and it booted perfectly. Note: the bois update did fix the SecureBoot nag.