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Forget it.
It seems to be an interaction of x264s mbtree feature, mencoder and converting DTS to 2channel MP3. I deactivated mbtree and it produced a flawless DTS audio mkv so far. (HD movies are not the best source when it comes to testing a script ;-) Even my slightly OCed Core i7 920 takes quite some time to encode a 2 hour movie in 1080p.)
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