It's odd... I tried to flash my the BIOS on my new GA-EP35-DS3L yesterday through @BIOS, which failed. Then I tried through Qflash (in-BIOS software) which failed too. Took a full CMOS reset before the board could recongnize the USB key I was using for the flash...
I use ASUS boards and never had to clear my CMOS after a bios flash - What I do after flashing is enter the bios, load defaults, save and re-configure bios again.
As far as the dual bios and crash free bios, it seems that more often than not, they are useless - I know cases of people flashing their bios and it failed, and the crashfree didn't take over to recover.
Try clearing the CMOS, if that doesn't work, consult your manual for the procedure - (moving of jumper, hotkey, etc.)
Also if your flasher fails to properly flash the bios all the time, you may have a bad EEPROM - this happened to me on an ASUS board years ago.