Old school pull out batter fix... lol. Newer mobo's usually have dual bios rom that is not volatile and will try and copy itself over leaving some nasty problems when a battery dies. ALSO, try and boot from CDROM without the HD plugged in, my bios actually copies itself to my HDD also in event of a catastrophe. HDD BIOS backups are a PITA to deal with though and have a high failure rate... Much easier to reflash.
Would you happen to have a Gigabyte mobo? Gigabyte has some well documented "black magic" bugs of not wanting to boot from a cdrom drive when bios gets corrupted... which in turn forces you to boot/recover from a usb drive with bios bin in root or sata cd drive with bios bin in root...
^DO THIS BOOT PROCEDURE BEFORE CLEARING CMOS! Gigabyte (idk about others) foolishly copies a backup in CMOS/HDD (dual chipped on newer models [bout time]) to use Q-Flash with. The issue sounds like more of a bin corruption than settings. Try and reflash with a CMOS backup before clearing it all-together.
*** Not responsible for your failed flash***