You can switch from using a virtual memory card to using a GCI folder by going to the GC configuration tab and changing the first memory card to the GCI folder option. Dolphin will then save GCI files directly to a folder instead of writing them to a .raw file.
Did you create your virtual memory card ahead of time, or did you let Dolphin create it when you were playing the game? You could also try deleting your MemoryCardA.USA.raw file, then using the memory card manager to create a new card with the same name before you play the game. It might be able to save correctly if the memory card already exists.
Did you create your virtual memory card ahead of time, or did you let Dolphin create it when you were playing the game? You could also try deleting your MemoryCardA.USA.raw file, then using the memory card manager to create a new card with the same name before you play the game. It might be able to save correctly if the memory card already exists.