Hey man had the same problem with mine a while back. you need Parition wizard. Just download it for free. I'm not on my computer at the moment but what you want to do is delete the whole sd card, apply that then format it to fat 32, primary, 64kb. Why mine was messing up was because when I used windows formatter it gave me logical which wii u and 3ds can't read you need it set to primary and it reads it. The wii u and 3ds have a every specific Parition. Primary is the dark blue color. It must be dark blue when it's done.
In the image first sd with the little Parition is what dark blue you want.