Here's how to know if you have the Cinavia problem, or the recent MKV muxxing issue.
If your file gives you grief right away....ie. no sound, or slow motion with tsMuxer right off the bat, the issue is with the muxxing, or writing of the file, and how the various engines deal with it. Generally a black screen, no sound, or errors left right and center.
Cinavia only appears after playing the file for 20 minutes, and there is the obvious Cinavia warning on-screen.
Again, the ONLY file/movie that I have confirmed is Cinavia protected, is THE LOSERS. All other recent MKV problems have been a writing or muxxing issue.
I thought, for a while, that REPO MEN and THE RUNAWAYS suffered from Cinavia, but it was in fact the way they were put together.