If you aren't afraid of using the Terminal, just use x264 and/or ffmpeg directly. Of course, OSX tends to be rather neglected when it comes to other people supplying native builds of those tools, so if you want to make sure you have the latest versions then it helps to learn how to build them yourself (but this might not be feasible if you don't have access to a 10.6 install disc or don't want to grab Xcode from the App Store).
Basically, set up MacPorts according to the instructions on http://davidbaumgold.com/tutorials/wine-mac/
(yes, it's a Wine tutorial page, but you can stop before Part 3 if you don't want Wine), and then use MacPorts to either A) get the necessary tools to build x264 and ffmpeg yourself or B) use the x264 and ffmpeg-devel packages that MacPorts itself provides, since those are fairly recent. For option B), all that would be necessary is to use the following command:
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sudo port install x264 ffmpeg-devel
And it'll install them for you. One caveat concerning x264 from MacPorts is that it most likely won't have FFMS2 input support or MP4 output. You have to build x264 yourself for those features, or rely on using libx264 through ffmpeg (which can also process the audio, if needed).
If A) seems to be the less confusing option, I can post the instructions I typically use for building x264 and ffmpeg, although it may need some tweaking because I usually don't build it for OSX. A couple of my other posts similar to this are here
, and here
. With said instructions, it would just be a matter of copying and pasting the commands into the Terminal.
I'm not sure of how 'correct' the output of MakeMKV is, so you might want to run the MKVs through mkvmerge just in case (I'd try the MacPorts method of installing it first, but there's also http://jonthn.free.fr/MKVtoolnix/
). That should clear up any underlying container problems that might screw with you down the road. This may actually be the root of the issues you're facing with Quicktime and MPlayerX, although I don't know why Finder would be OK with it when Quicktime isn't.
If the GUI isn't available from either of those sources, then you'll have to use the Terminal again. A simple:
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mkvmerge -o output.mkv input.mkv
should work. Perian and MPlayerX should be up-to-date enough to handle MKV header compression.