A nice guy by the name of Mosc has written a program that automatically un-orders the ordered chapters for you by scanning all MKV's in a given directory, and outputs a .bat file that runs mkvmerge a lot to put linked files back into normal files.
Download here:
http://upload.riposte.nl/upload/ChapterUnorderer.7z
Usage: chapterunorderer <source directory> <destination batch file>
(without <>'s)
Requires that dumpsuid and mkvmerge are in your PATH (current directory works for dumpsuid; the mkvtoolnix package automatically adds itself to the PATH when installed so mkvmerge should already be there).
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17:43:13 <~deculture> Also, TheFluff, you are so fucking slowpoke.jpg that people think we dropped the DVD's.
17:43:16 <~deculture> nice job, fag!
01:04:41 < Plorkyeran> it was annoying to typeset so it should be annoying to read