After checking some working source files and some source files with error here is what I found:
In working source files the track order is video track (id 0), audio track (id 1), subtitle track (id 2) and charter. In sources with error the audio track is first (id 0) and the video track is second (id 1). For me it looks like that this is the problem. After changing the track order of a file with error Ripbot encoded it without a problem.
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