Thanks for the xml files. Can you please activate debug logging in PMS ? Then, when playing above films, you will have an entry in Plex Media Server.log like the following one:
Apr 23, 2017 10:29:26.440 [0x7f1536fff700] DEBUG - Streaming Resource: Reached Decision id=7205 codes=(General=1001,Direct play not available; Conversion OK. Direct Play=3001,Not enough bandwidth for direct play of this item. Required bandwidth is 6145kbps and only 3000kbps is available. Transcode=1001,Direct play not available; Conversion OK.) media=(id=7533 part=(id=11693 decision=transcode container=mpegts protocol=hls streams=(Video=(id=9578 decision=transcode bitrate=2642 encoder=libx264 width=718 height=480) Audio=(id=9579 decision=transcode bitrate=203 encoder=aac channels=2 rate=48000))))
You can search the PMS log using "reached" as the key.
From your xml files (this is what I think, but I need this to be confirmed with the PMS log):
1) Skyfall - Has one hevc video track, and one aac 5.1 channel audio track. PlexConnect detects that hevc is not supported by the ATV3 and asks PMS to transcode. Video is transcoded to H264, but audio, previous to this patch, was transcoded to AAC-stereo and now is transcoded to AC3 5.1, so if your TV does not "understands" AC3 5.1 you will have no sound from it
2) Underworld - Has one h264 video track, and one ac3 2 channel audio track. PlexConnect detects that ATV3 supports this natively and asks PMS to DirectPlay the file. If you get sound from it is because your TV "understands" AC3 2 channel. If, instead of AC3-2ch the audio track was AC3-5.1 you would have no sound, even with the previous PlexConnect version, because PlexConnect would DirectPlay the entire file (video and audio)
What I am planning to do is to create a new ATV parameter (in PlexConnect settings) so that, by default, users with AC3 audio tracks get them transcoded to AAC (as happened in the past), and users with Dolby Digital capable players (AC3 5.1) can use that functionality.
Ideally I should pick the "ATV Setting" and not create a new "PlexConnect Setting", but the problem is that nobody (even Baa and roidy, the "parents" of PlexConnect) knows how to query the "Dolby Digital" status of the ATV.