I had fps issues when transcoding from avi to mp4(x264). Eventually the problem was in PTS and DTS values, so lines 12-15 where added before av_interleaved_write_frame function:

1.  AVFormatContext* outContainer = NULL;
2.  avformat_alloc_output_context2(&outContainer, NULL, "mp4", "c:\\test.mp4";
3.  AVCodec *encoder = avcodec_find_encoder(AV_CODEC_ID_H264);
4.  AVStream *outStream = avformat_new_stream(outContainer, encoder);
5.  // outStream->codec initiation
6.  // ...
7.  avformat_write_header(outContainer, NULL);

8.  // reading and decoding packet
9.  // ...
10. avcodec_encode_video2(outStream->codec, &encodedPacket, decodedFrame, &got_frame)
11. 
12. if (encodedPacket.pts != AV_NOPTS_VALUE)
13.     encodedPacket.pts =  av_rescale_q(encodedPacket.pts, outStream->codec->time_base, outStream->time_base);
14. if (encodedPacket.dts != AV_NOPTS_VALUE)
15.     encodedPacket.dts = av_rescale_q(encodedPacket.dts, outStream->codec->time_base, outStream->time_base);
16. 
17. av_interleaved_write_frame(outContainer, &encodedPacket)

After reading many posts I still do not understand:

1. outStream->codec->time_base = 1/25 and outStream->time_base = 1/12800. The 1st one was set by me but I cannot figure out why and who set 12800? I noticed that before line (7) outStream->time_base = 1/90000 and right after it it changes to 1/12800, why? When I transcode from avi to avi, meaning changing the line (2) to avformat_alloc_output_context2(&outContainer, NULL, "avi", "c:\\test.avi"; , so before and after line (7) outStream->time_base remains always 1/25 and not like in mp4 case, why?
2. What is the difference between time_base of outStream->codec and outStream?
3. To calc the pts av_rescale_q does: takes 2 time_base, multiplies their fractions in cross and then compute the pts. Why it does this in this way? As I debugged, the encodedPacket.pts has value incremental by 1, so why changing it if it does has value?
4. At the beginning the dts value is -2 and after each rescaling it still has negative number, but despite this the video played correctly! Shouldn't it be positive?