Okay, I did some testing and I successfully restored a save to my retail cart, unfortunately it was a brand new save I created using a ROM, the odd thing is that PokéSav can read my backed up save so I don't know what's happening here.
Oh, I did this using WiFi-FTP mode, as 3 in 1 mode gave me an error.
Edit:
Keep trying until it reaches 100%, it happens to me as well.