I did a format but didn't fix anything, so i tried with a new SD card and now the problem disappeared.No, it needs to be FAT32 or the 3DS can't read it. A reformat (still on FAT32) might help.
My old card was a Lexar class 4 32GB SDHC, i wonder if it had compatibility issues with the 3ds or was simply faulty. Doesn't really matter anyways now, thanks for the help.