analog said:
I was going to try this for kicks, just to see if it'd work, but get a "matroska parse error: invalid h264 NAL unit size. NAL unit truncated" error :(
Just open the mkv with mkvmerge GUI or MKVExtractGUI2 (both part of the free MKVToolnix package) and mux it again. Then try again with tsmuxer. Worked for me. :)
Edit: Harmy beat me to it.