I downloaded the brand new version of VBA-M: SVN1025. It has a new bug, though. If I play any GBC game with an internal clock in it (namely Pokémon Gold/Silver/Crystal or Telefang), I get this error message:
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Battery file's size incompatible with the rom settings
Warning : save of the battery file is now disabled !
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It still loads the save, but it cannot make a new save at all. I'm guessing this has to do with the fact that saves for games with an internal clock have slightly bigger filesizes?
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GBA games, such as Pokémon Ruby/Sapphire, are not affected.
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And just so people don't say "This works fine for me," I was running this on Windows 7 64-bit. Hopefully I'm not the only one who experiences this glitch.