I see the following behaviour in MT 0.11.0:
When configuring a directory for inotify as scanning option and the directory has one or more subdirectories which can not be watched by the MT user (e.g. lost+found which can be only accessed with UID 0) the thread will abort with the log line (caused in AutoscanInotify::threadProc() line 335):
ERROR: Inotify thread caught exception: no permission
The result is that the directory is no longer watched and no changes are recorded.
A possible solution would be to log the name of the offending directory in the log file and proceed with adding watches where it is possible.