Audio not working with MKV containing DD TrueHD stream

I am able to use TrueHD only when the audio is set to manual passthru with the appropiate boxes checked and only when I use my NAS running twonky server for both mkv and m2ts files. If audio auto is selected or I access the shared NAS directly TrueHD will not play. I have used several programs to make the m2ts into a mkv and the audio stream is still available only when served audio manual via twonky.