I have to make sure the AC3 is set to passthru and set the second audio track to a delay of 0, otherwise it defaults to 65515ms delay, which is a little over a minute. MkvToMp4 seems to be doing the trick as long as I remember to set the audio tracks correctly. I've tried using VLC to convert but I lose secondary audio tracks and still loose chapter markers. I've tried extracting the MKV streams and muxing them to MP4 using MP4Box GUI but the audio track are out of sync and chapter markers are lost The movies I want to convert typically have an AC3 6-ch track, ACC Dolby/Stereo track, and will have chapter markers. Without going through the hassle of a full re-encode, I'd rather convert them to MP4 without losing chapter info, audio tracks, etc. If the movies are in MP4 then the Samsungs work fine.

On the Nexus, opening the file opens VLC without issues.

I have VLC on the Samsungs and it will play them fine as long as I go into VLC to open them but not through the file manager.

Although I have no issue with my Nexus 7, the two Samsung tablets complain about MKV files. I've been using Handbrake to convert DVDs to use in tablets for traveling.

Convert mkv to mp4 handbrake