I ran into an apparent bug where files in directories that used to have overly restrictive permissions would not get picked up in subsequent scans. This was in version 5.3 (build 4568) on Arch Linux. Try this:
1. On a Unix-like system, add a directory under the media directory with permissions set so that the subsonic user does not have read (r) or execute (x) permissions. Put a music file inside that directory.
2. Start a scan of the media directory. The new folder name may appear in the sidebar of the player, but it will not have anything inside
3. Change the new directory's permissions so that subsonic has read and execute permissions.
4. Start a scan again.
Expected result: The music file is now available in subsonic.
Actual result: The music file is still not available. Renaming the folder and rescanning will let it appear.
It appears subsonic is remembering the old permissions and skipping those directories it thinks it can't access during the scan, even when the permissions have been changed. It should probably forget what permissions directories have altogether.