Oh that's maybe because atmosphere changed the folder name. Now you need to install to "atmosphere/contents/*titleID*" folder. The mods and everything should be the same inside, they essentially just renamed the "titles" folder to "contents". If you updated atmosphere it automatically moved your currents files over to the new folder, but if you add more you need to put it in there and delete any "titles" folder since it's no longer used by atmosphere.
I'm assuming that's the problem but if you use any other cfw then it stays in the "titles" folder so if that's the case check your file names and what case they are in.
Thanks. I got them working now. I messed up the folder structure and forgit the NX folder in the hierarchy.
I also am using simple mod manager for this so i can turn the mods off if i need to
Thanks