It is probably because the extensions are uppercase, I have a patch added for this in my dev branch but since you should be using lowercase extensions, well at least if your WordPress install runs on linux, I haven’t really made the effort to push it through. Since I do not have much other time to add more functionality lately and making a release for just that is a lot of extra work/headache since it is technically behaving as I believe it should. If you upload files with lowercase extensions and you are still having issues please let me know.