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#11
If you use Metafox (download it from my tools page), it will extract the audio/video streams from almost any container (avi, m2ts, flv etc) and place those contents into a MKV.
To use it, just install it. It places a shortcut on your desktop. Drag and Drop any file to the shortcut, it automatically makes the MKV in the originating folder.
EDIT: you will need my Win7codecs installed for formats like FLV to extract properly.