When mediatomb scans a directory using inotify scanning, and it encounters a directory it does not have access to, the inotify thread terminates.
This in turn means that no updating of the directory contents are performed.
The error logged be mediatomb is:
ERROR: Inotify thread caught exception: Permission denied
The attached patch solves this problem, by making Inotify::addWatch return -1, if EACCES is returned by inotify_add_watch. It also logs the access problem to the logfile, using log_warning.