Something must be off then. Uncertain whether its the player or software settings or combo of both. I currently have over 550 movies (approx 70% are Blu-ray) that have been handbraked to m4v's. All of them play audio perfectly. First track is always 5.1, 2nd is dolby surround II. System is aTV3 connected to a Sony AV system via hdmi 1.4. Using Plex & Plexconnect. YMMV 😀
Oh, believe me - I could write a book on variable mileage. I used to beta-test firmwares for Popcorn Hour, and man... the number of things that can be working for one guy but utterly crocked for the next is dizzying. I've come close to tears, at times.
I do have another problem that is personal to me - I have a particularly acute sense for duff audio-sync. In blind testing, I can spot delays of 20ms (one of the reasons why I got the gig for beta-testing, I think...). I can be watching something with other people and say, "Christ, this is unwatchable...!!!", and they'll not be able to see what the problem is.
I do not consider this a gift. It ruins my enjoyment of movies and television.