Hi Katsushi,
I am very interessed by your plugin because it perfectly answers to what I want to do: modify the architecture of the folders under /uploads and get the URL of the media automatically modified in the posts.
But I confirm it does not work also in my config. The folder is physically created but not seen in the Media Library. I am working in a Windows 7 local environment using XAMPP.
imho the issue comes from a recent modification of the Media Library management in WordPress