How can I check it? It's this one. Don't know anything about an additional encryption.
https://code.google.com/p/nintendon-t/source/browse/trunk/kernel/main.c#159
error -3 means it could not mount the FAT partition, the nintendont kernel (running the game) uses a different FAT driver which is not as forgiving as the one used in the loader, so maybe you really should try to completely reformat the drive with something like easeus partition manager just to make sure the partition table is as simple as possible to read for the kernel.