Several 2SD users are experiencing problems while others work just fine tho. So it might happen.
But as guitarheroknight said, checking your SD card and your mSD card (if you're using the red card) might also be good. I've heard of people formatting sysnand and emunand and getting improvements afterwards too.
Then it's probably as I said before, some unknown bug still affecting you like some other 2DS users are experiencing. It doesn't seem to be something common to all 2DS users though, which makes it even more strange.