Yep I read it but probably skipped the "on my Gateway" part.
Every 3DS mode flashcard saves but the save function gets "destroyed"/ not triggered when using NINJHAX.
@OP You have to use a hacked save. But I dunno if you can get it anywhere.
I tried starting cubic ninja, then using the home button to have the save file there, then did the QR code but I still have to do it everytime. I just did what iwasaperson suggested a day ago and that seems to work. You need the .cia for a gateway.