I swear everyone around here would rather work harder than smarter. All you guys had to do was go to eShop to repair your software, go into the game and resave, and then load PokeBank and it would have recognized the save. Also, the update was both a FULL new install AND an update, I suggest uninstalling it first altogether and then doing it. I had the exact same problem and everything I did worked just fine (even after save editing they don't always show up, I have to go in game and resave, then they do). But you know, do whatever works for you.
PokeBank is weird.