por que não usar o mkvmerge? link
mkvmerge.exe --output E:\output.mkv --audio-tracks 1,2,3,4,5 --no-subtitles
--no-chapters --language 0:und --default-track 0:yes --compression 0:none
--language 1:eng --track-name "1:5.1 AC3 Eng" --default-track 1:yes --compression 1:none
--language 2:eng --track-name "2:5.1 DTS Eng" --compression 2:none
--language 3:eng --track-name "3:2.0 DTS Eng" --compression 3:none
--language 4:ita --track-name "4:5.1 DTS Ita" --compression 4:none
--language 5:ita --track-name "5:2.0 AC3 Ita" --compression 5:none "file1.mkv"
--track-order 0:0,0:1,0:2,0:3,0:4,0:5 --probe-range-percentage 0.50