The board will be looking for AWDFLASH.exe, which is the normal AWARD BIOS flashing utility, and the BIOS file itself to be on the disk. Might be best making the disk yourself rather than using the one that tool makes, just grab a copy of AWDFLASH.exe (should find it on most mobo manufacturer's websites) and put the .bin file for the BIOS on there, just those 2 files, and see what it does. In fact there might be some info on what filenames it will be looking for in the manual.
Edit: That's assuming, of course, AWDFLASH isn't on the floppy already, if it is it's deffo RMA time.