It had everything to do with the version. Nintendo could ban you because of the following reasons: (AND I DON'T KNOW WHY PEOPLE THINK NINTENDO ONLY USED 1 METHOD TO BAN PEOPLE. THEY CAN USE A COMBINATION OF ALL OF THEM).
- The leaked CIA had version as 0. Therefore it was obvious that you pirated the leak and used it as CIA instead of a cart.
- Also, by playing via CIA before the game was released on Eshop, you basically told Nintendo that you were a pirate (you cannot have an Eshop game before release unless you pirate it).
- Nintendo also banned people for playing early before release date, retail cart or not.