I don't know how Absolute Zero's patcher works.
The ones we use ensure the checksum matches that of a properly ripped retail disc to avoid problems and false bug reports. If it doesn't, it doesn't patch. The only advice we have is to go buy the game proper and try again. There is nothing else we can do to help you.
Well, I went ahead and downloaded a copy of the bin on the internet and patched the game. It worked flawlessly. Like hell i'm gonna buy a game that'll never be released outside of Japan just to appease overzealous patchers.