Return of the Missing Audio Elements
I thought this had been fixed, perhaps by commit ec76be3f, but I had it again earlier this week.
The issue appears when using mkv and when a broadcaster switches from, say, stereo to 5.1 AAC sound - for example, between the continuity announcement and the main film. The BBC HD channels appear to do this on both satellite and terrestrial.
Anyway, tvheadend initially identifies the stereo stream, but seems unable to record the other channels when they appear later on in the programme. VLC can see the stream changing (from Stereo to 3F2R/LFE) but the other channels don't come through, so you're left with only 40%ish of the soundtrack - all dialogue is missing. I've tried it on XBMC, VLC, BSPlayer - no dice on anything.
Cutting the file within the 5.1 "limits" (i.e. deleting all stereo segments) with mkvmerge doesn't help. Attempting to re-encode with Handbrake or FAAD/aften doesn't help either (it may well be that those extra channels simply aren't there).
I seem to recall that it's a limitation of the mkv container (although Adam will correct me here - he's done it once or twice already on this topic! ), and I thought that John had worked around this - perhaps by using chapter markers, which is why I identified the above commit. Raising here in case something's gone awry, but it may just be that mkv isn't the right container for variable streams and users need to know that.
Some relevant history: