You need to Download that Specific Version of AFLASH2 from my Link and Follow those Directions EXACTLY. This seems to be a problem with Many ASUS Boards. Try that and report back.
I did downloaded the version of AFLASH2 on Rapidshare called Ali-aflash2.rar from your link, and in fact it was the same one I already had.
As long as you can Boot From USB you should have No Trouble using it to Recover from a Bad flash. Just Flash the modified Bios from the USB in DOS with AWDFlash and it should NOT cause any problems.