I have created an autoscan on a directory 'tv' which has a series of subdirectories, each with a number of video files. When the autoscan runs, some files are set up in Video/Directories/tv/Dirname (as on disk) but about 10% are in Video/Directories/Dirname. I've tried deleting the database and re-adding (I use a timed full recursive scan). Mostly it's the newer ones which are chosen to be in the rogue directories, but this is not consistent, and in one case these files were all larger than files of similar age which were not chosen. But, in other cases this rule doesn't apply. Very odd. None of the files or directories are symlinks.
Also in some cases there is an extra directory level: files are in tv/DnameA/DnameS6 and in that case the 'rogue' files appear in Video/Directories/DnameS6.
I've looked in the database, and the view there seems to match exactly what I see in the directory browse; only interesting thing is that the two instances of 'Dirname' (with two different parent_id, each containing its own subset of the actual files) have the same update_id value.
I'm running ubuntu 12.04 and mediatomb 0.12.1-0ubuntu4 on x86_64.
I was using the same setup with 10.04 for a while, and it seems to me that in that version *all* of the files were in Directories/dirname (the actual disk hierarchy was not reflected).