What I found odd is that I tried playing Yokai Watch, it prompted me to update it? I'm in EU and the game is JPN (.3DS), so I click Y to update, says it has applied the patch, but still, the message is there for me to update it.
When I play Dairantou smash bros and it prompts me to update, it just says that it can't find the update in the eshop. Odd that yours says the patch has successfully been applied.
