I'd suggest you use .ts then and pretend you never saw anything :p
The mkv container option is a great idea, as I much prefer it to anything else, but I abandoned it some time ago because of various quirks and issues. Unless you really need to use it, I'd genuinely recommend looking at .ts as a default, it's less troublesome.
That said, .ts can sometimes have issues of its own because the passthrough means the streams are saved along with any timing errors, which remuxing at source seemed to cure for me. Not really a problem unless you want to edit the file.