You should twiddle with mencoder (it's a part of mplayer package). Executing 'mencoder sourcefile -o destfile -oac copy -ovc lavc -sub subfile' could get you somewhere. If not, try with different font switches, as well as experiment with codecs passed to -ovc (I've experimented a bit and it seems subtitles aren't added when video is simply copied). You could also use -vf expand x,y to put the subtitles *beneath* the video, not over it.Well, it surely needs some twiddling on your side ;-)
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