I've faced a similar problem before. I was just doing stream copy i.e
changing the container format to avi. 
I think you care correct your pts and dts may not be correct. I  too ended
up playing with various combination.
Try following. it worked for me. This is just for stream copy which involves
no decoding
 outpkt.pts= av_rescale_q(inputpkt.pts, input_video_strm->time_base,
output_video_strm->time_base);
Similar rescaling for dts. Also you will need to do it for audio stream too.

One thing to note it that if you are encoding decoded packet then you can
forget about pts and dts. Encoder automatically does that for you.
Pradeep




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