I know this thread is old, but I just had the same issue. If anyone can help, it would be appreciated.
(I tried this on multiple O3DS, all on latest B9S 1.3 and latest Luma3DS 10.0...)
UPDATE: Apparently there was something wrong with the cia file I was trying to install.
I used Godmode 9 to rip the update off a separate 3DS that had it already installed and that cia installed fine. I think the 3DS that already had it installed had it from the FreeShop days and the cia I was failing to install was downloaded elsewhere.