NMM is not really a memory card emulation.
It's saving the game's save data directly as files, instead of using the card or an image of the card as binary container.
Each game has its own files and don't share them with others, and there's no memory card format (the format is FAT32, as it's stored directly on SD or USB)
That's why some games doesn't save correctly (Mario Kart Double Dash uses characters for the filename which is incompatible with FAT filesystem, so it saves but can't open it as the filename is corrupted).
Maybe that's the case here, it's trying to save the files with filename in ShiftJis, or Euc, or anything using a double char, but it doesn't save correctly on FAT?
it would require an USB gecko to check what happens when you save and compare the logged filename with the one stored on your SD or USB.
That's why Nintendont is now using a binary image of the memory card instead of NMM.