OKay, I figured it out, or rather found a workaround.
Incase someone ever googles this and curses beause of the lack of answers:
I simply got rid of the offending first track by using the mkvtools:
mkvextract tracks myFile.mkv 1:video.mkv 3:audio.ogg 4:subtitles.srt
This extracts the tracks 1 (video), 3 (japanese audio) and 4 (the subtitles) from the original files.
Then I splice 'em together with
mkvmerge -o copy/myFile.mkv video.mkv audio.ogg subtitles.srt
Presto, the same thing with the first audio channel dropped - ViddyUp can hand candle this, then.
Note that there's no re-ecoding involved until I use ViddyUp, since I just take things out of a contaner and put a nw container together.
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