Some ideas:
* Some file types are not supported (not mp3/(m3a/m4p/wma), e.g. you have .ogg or .flac or .mpc or .shn …. files. These are not set for scanning/transcoding.
* Access rights, though Firefly as a service should have sufficient on Windows
* Have you tried to find a few of those songs not served, to see if they fit into the first category (different type), have other special properties (special characters, broken tags, etc.)?