h264 TS remuxed into MKV with MKVToolNix -> corrupted frames?

[NailBomber]

Greetings.

I have a lot of captured livestreams from YouTube which are h264 TS files.
A lot of those files have wrong duration and seeking problems. They can be played from start to finish just fine, but not seeked.
Remuxing them into MKV using MKVToolNix results in videos with correct duration and seeking, but they sometimes have a lot of visually corrupted frames.
Example: http://s013.radikal.ru/i325/1510/af/7d1a62646eac.jpg

Playing both videos (original TS and remuxed MKV) back to back with MPC-HC I see that original TS is completely free of such errors.

I assume this can be fixed by transcoding original video stream with use of DSS2, but is it possible to fix it just by remuxing it?
Why is that remuxing a video creates such corrupted frames in the first place? Current state of libav/ffmpeg decoders?

[LigH.de]

If MPC-HC (using LAV Filters) can play them, there is a good chance that ffmpeg may be able to remultiplex them, at least worth a try; multiplexers got many fixes during the last years. Another possible way would be using VLC to convert. And there are even more tools able to demux the H.264 video stream or remultiplex the TS (and possibly repair some features), how about TsDoctor before converting?

[NailBomber]

Thank you LigH.de!

Following your advice I downloaded latest nightly build of LibAV. Then I used avconv.exe to remux faulty original TS. There were lots of warnings like:
"[mpegts @ 000000000062e9e0] Continuity check failed for pid 17 expected 7 got 0"
, but resulting TS is free of seeking/duration issues and has no corrupted frames. Then I tried to remux it into MKV - again, no issues at all.
So does it mean that MKVMerge has problems with remuxing TS files? I used latest MKVToolNix.

Again, thank you very much!

[LigH.de]

MKVMerge seems to take timestamps very important. And when you try to convert a cut and joined video with gaps in the timestamps, you may have to set up MKVMerge to ignore timestamps not to get confused and to rebuild a contiguous time code progress.