Mkvtoolnix

Free open source cross platform set of tools and utilities for working with mkv container files. These tools are ideal for working with H.264 video in an mkv container.

(additional info coming soon...)

Uses

remove a subtitle track from a Matroska .avi file

note: It is recommended that you disable "header removal compression."

Run mmg.exe which is a GUI front end for the tools. open your mkv with it. uncheck whatever you don't want and then give it an output folder and name. click merge.

source: aedipuss on videohelp.com

support

header removal compression bug

Starting with v4.1.0 Mosu, the developer of mkvtoolnix, implemented “header removal compression”. Several hardware/software players don’t support header compression in mkvs. The benefit from header compression is minimal at best, it is best not to use header compression at all for compatibility purposes.

source: MKV Mania: Header Compression And The Side Effects by Damian

Version 5.8.0 allows you to set a default -
Run mmg.exe and open file options and put a check in disable header removal compression. Close mmg and then restart.