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Posted the answer for @SergioBasurco, so that he can accept the topic with a solution.
I just tried to answer to my own question but I can't since I'm a new user... it was a long post and went away :( Anyways, for those who need a solution asap, I solved it using gstreamer + openCV, which uses ffdec_h264 (from ffmpeg) as decoder, so I don't know where the bug is coming from and don't have time to debug it all over OpenCV. Gstreamer getting started How to merge it with OpenCV. I hope it helps someone, I'll file a report and answer here with the feedback when I have some time.
