Are you installing .cia theme packages? If so, I had the same problem - fix it like this:
1) change your current theme to the default
2) go to your .cia installer and delete the program with unique ID "0x0008f" (the product code should be CTR-M-HMME-00; this is the USA 3DS' theme file)
3) install your new .cia package
You will lose the eshop themes you downloaded beforehand (because you deleted your old theme package). You'll have to have a copy of your eshop themes and pack them with the custom themes to get them back on your system.