Convert TsMuxer .mkv to MEncoder/Avisynth .mkv -Best method?

[coolcat]

I have an mkv which I can only play on PMS if I select transcode and select TsMuxer. However, in TsMuxer the subtitles don't show, so I was just wondering what's the best way to get the file to play via MEcoder or MEncoder/Avisynth? I don't want to loose any quality and the file is about 2gb. Thanks for your time