I also have the version with the different intro than the japanese one, so wondering the same
I found the following:
-version 1.0/prototype plays music in a different order than the OST (perhaps some music is even missing); ex. the stage 6 theme plays in stage 2
-version 1.1 has the correct order, the game-start message is different, and the other changes mentioned above
-version 1.2 appears identical to 1.1 but harder, this could even be some crazy hack but the MAME team sure seems to think it isn't so I'm just calling it 1.2 anyway