Passthrough (.ts) should be just as it was broadcast - so you only have something flagged as encrypted if that's what your broadcaster sent out.
mkv - that message means that you've got an audio stream that hasn't been tagged by your broadcaster with a particular language (including audio described). VLC seems sensitive to that.
I don't know what will play your streams (well, XBMC will, but that's perhaps overkill) - SMPlayer, maybe? - but mkvmerge GUI/mkvtoolnix will re-tag the offending audio stream, or strip it out entirely, and you could do that as a post-processing job to automate it. The .ts stream is more clumsy, in that you'll probably need to re-encode it to get rid of any broadcast errors: Handbrake will do that for you, but it'll take time.
