Always flash from DOS. Btw, that last part remained same in your case as both the original & modded bios has same data in that portion. So the part wasn't updated.
As you have already flashed the modded bios, thee s no need to repeat that. FYI, you need to copy AFUDOS & SLIC.ROM (autoexec.bat is optional). autoexec.bat executes at first & runs the command which is specified in it. Personally I prefer to do it manually i.e type the commands in DOS prompt.
afudos is strange.. usualy u need space after / in most dos progs. with afudos it uses /iFILENAME toghether.. its how its designed.