You gotta clear your icon cache. You have to delete CacheD.dat located at "SD:\Nintendo 3DS\[ID1]\[ID2]\extdata\00000000\0000008f\00000000\00000005"
Note, I'm assuming your console is North American. If EUR, the 0000008f folder is 00000098, and if JPN it's 00000082. In any of those folders, you wanna delete the file "00000005".
Please also note that this'll remove your current theme, but won't actually delete any themes. It won't wipe shuffle theme preference either, you can go right back and set it to what it was, if anything.