I guess my TV only supports Dolby Digital 5.1 (i.e. not 2.0), as 5.1 plays correctly? With DD 2.0 mkv file:
ATV DD setting: Auto, Plex DD setting: On - Paused video
ATV DD setting: On, Plex DD setting: On - Video plays, but no audio
ATV DD setting: Auto, Plex DD setting: Off - Video plays with audio