I'm using Handbrake to do the conversions (MakeMKV to extract a full copy of the BD to my computer).
It might be the DTS-MA track that is causing the issue. Anything that wasn't a standard DTS track for me seemed to be a problem when I tried to do playback in VLC (no audio for any of the tracks). So, I only ever select standard DTS as my source for all audio tracks.
Also, one of the newer annoyances for me in iTunes 11 has been any movie I import into the Library gets filed under the "Home Movies" subsection, vs just standard "Movies". When you drag and drop it in, are you looking for the new movie in the Movies subsection (ie, Movies->Movies)? Are are you checking under the List view (ie, Movies->List)? These WILL NOT show in the Movies subsection by default until you change the Media Kind option to "Movie" in Get Info area. Check the Movies->Home Movies section and see if your media is there.