Problems saving on auto save?

Does this emulator have issues with auto saves?
It took me awhile to set it up, but now it works perfectly for Pokémon Emerald. If I save in game, then save on the emulator, everything’s fine.

But when I play Yugioh - The Eternal Duelist Soul, a card game that automatically saves after every round, I can never save my progress. It always deletes my file.

Am I doing something wrong, or do auto save games just not work?