Then you don't do it right. The correct and safest way to flash the bios is this:
1. clear CMOS to complete restore original settings and making 100% no settings will be "hardflashed" into the BIOS (happened for me on my NF7-S v2.0 when I forgot to clear CMOS first and ruined the DDR speed settings totally).
2. start the pc and flash the bios in DOS (I never had and never will trust windows flashing utils, DRDOS along the with flashing tools is the way to go).
3. boot up, enter BIOS do "load setup defaults", save&exit
4. enter BIOS again, change settings and enjoy a good flash with no problems...