something i came across with FBI is, if you boot straigh into HBL without entiring the SYSNAND once, you might fail to install some CIAs.
so the solutio is really simple, boot your 3DS into your SYSnand once, they use whatever method you have to entire HBL(ofc not the restart method, you can use cubicninja or browserhax)
then start using FBI to install that CIA.
i found this when i am trying to do a (flashcart-free crack on my 9.1N3DS)