It seems as though I did something wrong with Trailer 2 for Captain America: Civil War. Sync was off as was the frame rate, I am happy to say that I believe that the issue has been fixed, and new versions are now available at the Captain America: Civil War page. I am not quite sure what happened, but in the end I had to add a delay on the audio for the .mkv, and then used Handbrake to create the .mp4 from the .mkv file. These files play back in Plex and VLC without issues.
I mentioned that I have had a lot on the go lately, and part of that is due to a pending move – once we find a buyer for our house. The plus side to this is a happy wife, but also the ability to build a proper home cinema. I think it will be an interesting process, and I will document the journey here as I go along.