Also the latest Nightly Build is “affected”. Same issue.
If you search in the handbrake forum you will find a topic on this “issue” (I found it yesterday).
The “solution” for me is to do a final pass with mkvmerge because it solves it, for my point of view this issue could be correlated to the header compression. I don’t see any other thing that could be because the issue go away with just this “trick” (mkvmerge).
