Q: M4V/MP4 support on MacOS Sierra broken?

I have a decent movie collection I started some fifteen years ago. Whenever I purchase a DVD or BD, I digitize it, specifically into a m4v container using h.264 compression. The system has worked for years, and my AppleTV's have happily supported all of my media.

On El Capitan, all of my movies played on iTunes, Quicktime, AppleTV, and even Plex. Both mp4 and m4v. (both use h.264 compression, but m4v and mp4 containers differ slightly). When I upgraded to Sierra, I noticed the album art wasn't showing up in Finder or in iTunes. When I try to play certain movies, Quicktime fails. iTunes can't play them, and neither can Plex. VLC plays everything fine. It's happening on about half of the titles. They are encoded the same, and it makes no difference whether they are HD or SD. It happens on multiple systems, on have Sierra in common. They all have the same behavior, exactly. I restored my media server to the day before Sierra, and everything is working again on El Capitan. It doesn't appear that Quicktime has changed. All I can think is that Perian finally broke, since it is no longer under development. What puzzles me, is that I shouldn't need Perian for m4v, since this is a Apple supported format.

Any ideas on what the heck happened to h.264/m4v/mp4 support after the upgrade? Is anyone else experiencing this?