Then, have you tried to demux to elementary streams via eac3to and after remux/cut with TSMuxer?
i.e.
My input file "trial.ts" is under C:
and my output folder is "trial_out" under C:
And demuxing with eac3to:
Code:
eac3to v2.68
command line: eac3to\eac3to C:\trial.ts 1: C:\trial_out\video.h264 2: C:\trial_out\audio.ac3
------------------------------------------------------------------------------
TS, 1 video track, 1 audio track, 0:01:16
1: h264/AVC, 1080i50 (16:9)
2: AC3, German, 2.0 channels, 448kbps, 48khz, dialnorm: -27dB, -603ms
[a02] Extracting audio track number 2...
[v01] Extracting video track number 1...
[a02] Removing AC3 dialog normalization...
[a02] Applying (E-)AC3 delay...
[v01] Creating file "C:\trial_out\video.h264"...
[a02] Creating file "C:\trial_out\audio.ac3"...
Video track 1 contains 3779 frames.
eac3to processing took 22 seconds.
Done.
And remux them back to ts (or m2ts) with TSMuxer; you gonna see there won't be any problem left.