Same problem here. Here is what I have found so far.
m4v files are now capable of storing the original DTS soundtrack. So if the encoded m4v file contains only AAC and AC3 soundtrack, the file is recognised by iTunes and QT and will play file. However, if you are an enthusiast and retain the original DTS soundtrack along with AAC and AC3 in your m4v file, it will behave as indicated by Sastei and shall not be recognised. Why retain the original DTS soundtrack - future proofing since DTS is encoded to a higher bit rate and my encoding SW only allows upto 640 kbps on AAC and AC3 soundtracks (ST).
Now, before Sierra, other OsX had no issues with m4v files containing original DTS ST, but Sierra has an issue. I raised this as a problem while I was running beta versions of Sierra, but Apple has not gotten to it yet and I don't know if they will.
You may try to see if the m4v files you have that are not recognised by iTunes / QT have a similar DTS ST problem. If yes, you may re-encode these files by removing DTS ST using Subler. Not ideal solution, but works for now.
In my case, I would rather wait on Apple to fix it than lose my DTS STs.