Get it from here and put all of its contents into the bin directory (if it requests a password for the package then use ). It's this what makes this whole remuxing process possible without having to add too much user required input. You will also need a little package that will do some pretty smart "magic".You can get it from here and copy the executable (and any *.dll file, if present) into the bin directory.
Save it as mkv2mp4.bat and it's version 1.03 at the moment. Firstly you need to grab the script itself from here.Where as in my complicated guide you are just switching containers. However if you want to add subtitles (which are found as softsubs in the MKV file) then it's the only way, unless the XBOX360/PS3 magically supports TTXT (no it doesn't, been confirmed). You just have to note that by re-encoding the video you will lose quality.
Take a look at the next post where GHDpro has already started with a simpler guide than this one. Otherwise re-encoding the video stream is another possibility. Some tweaking is needed, whether you like it or not. This fact makes it really hard to just switch containers just like that. If someone who knows this well, feel free to explain it please. I don't know the exact specifics how it does this, and why exactly this happens (drops duplicate frames?). Even if you encode a stream at a constant framerate, for example 23.976 frames per second, it will end up applying a timecodes file to the stream. One of those would be the fact that it uses a timecode file on the video stream, to specify which sections/frames are played at what framerates. You have to take into account that Matroska (MKV) uses quite a few smart features which make it rather hard to convert.