Have you ever installed themes previously? I noticed when I made a pack and installed it but wanted to add more it wouldn't work until I uninstalled themes first.
Go to system settings, data management, Nintendo 3ds, downloadable content, and delete theme.
After that just use fbi, bbm etc to...
Okay I think I realized, make sure you still have the sub-folders, you need to have Custom, Custom NSFW, and Oficiales in there exactly like the example. I just tested by checking the entire example folder and it worked. Put your themes in the correct sub folder within that