When you try to play an MKV, does an error message pops up ?
If yes, please post here that message.
The difference between the two files it's not in size but in filters requiered to be able to play the files. First file needs an MKV splitter, an AVC decoder and an AAC decoder, while the second one require a simple MPEG4 decoder and an MP3 decoder.
If you allowed internal filters to be installed, you should check in:
-ffdshow video options that it is set to decode H264/x264/AVC
-ffdshow audio options that is set to decode AAC
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