Now if you cut such a PES stream even on the GOP boundaries, not
only the PTS offset of the audio to the video makes trouble but
also the broken subframes of audio Mpeg2 and AC-3 within the payloads
are the cause of noise at the cut mark (OK the bitstreamout plugin
ignores broken AC-3 frames but the Mpeg2 audio decoder on the DVB
card does not).
Well, one solution would be to extend the interesting part so that it
starts/ends on an audio frame that is related to the video frame. But this
sounds to be a different story.