The left side is just showing the PC directory where I FTP'ed the xorpad files from my 3DS for safe keeping.
You can ignore those.
I included it in the photo so you could see that it really does actually work on a N3DS and will create xorpads files.
All you need on the 3DS is a directory named 3ds and the current decrypt9.3dx file in a folder in it.
Maybe try re-downloading the posted below link decrypt9.3dx file to make sure you have the latest one?
(Correction, I'm using this one)
http://gbatemp.net/threads/creating-a-north-american-non-xl-new-3ds.381775/page-10#post-5426550