I'm not sure on this and you may need to wait until Dark Mantis or someone with a bit better Knowledge than me on this,but, what could be happening here is that you now have 2 different bios versions (one on primary ie: newer bios version, and an older version on the backup bios chip) and there could be a bit of a conflict at bootup if there is a problem with the flash...Maybe, I am just speculating here and don't want you to flash over your backup bios to match the new one if the new one is buggy.
As for future flashes it is recommended to use Qflash and not @ Bios because @ Bios is windows based and can be very flakey and brick your board!!!
You could try reflashing using the Qflash and make sure you Disable the 'Keep DMI Data' before you do it. See if that helps you.
Go here to learn how to Qflash
http://forum.giga-byte.co.uk/index.php/topic,2441.0.html