Muxing TrueHD only files creates cues that point to non-key frames
TrueHD is one of those audio codecs where not all frames are key frames. Mkvmerge knows this and tags them correctly. The problem arises when it creates Cues, as it doesn't ensure they point to keyframes. It just adds one Cue every 2 seconds worth of audio, not caring about the type of the frame the Cue ends up referencing. This is not ideal as decoding for TrueHD streams must start at a key frame.
You can reproduce this by muxing sample.thd.