ffmpeg muxing to mkv container

Question

I'm muxing H264 frames with alaw audio frames coming from the RTP stream but I'm having some problems with setting fps for the mkv container.

For the AVPacket::pts I am using the calculated presentation time (from RTCP SR reports) I am rescaling them as follows ( I had assumed exactly the same for audio):

pkt.pts = av_rescale_q(s_video_sync.fSyncTime.tv_sec * 1000000 + s_video_sync.fSyncTime.tv_usec, 
av_encode_codec_ctx->time_base, video_st->time_base); 

• the timestamp in the end is in microseconds (the first parameter) in theory it's NTP derrived.
• av_encode_codec_ctx->time_base is set to {1,fps} where fps is depending on the stream, let's say 5
• video_st->time_base is auto se to to {1,1000} (I gather that this is forced by mkv container)

I gather that this is what should be set to te rescale function (at least that's what examples show), but the ffprobe show strange readouts for duration and fps is set to 1k... and well the video plays strangely.

my question is how should I approach this? Should I rescale the timestamp to start counting from 0 for the first packet, or I'm messing two different time domains and thus muxer can't figure out what to do?

EDIT1:
I have figured out that since the timestamp is in micro seconds (and I'm not encoding) I should use {1,1000000} as timebase for pts calc instead of codec's timebase. Now at least the duration is ok, and audio plays smoothly, but video is 'choppy' there is a timestamp in the video that does not increment smoothly... and the fps is still 1k

EDIT2 It seems that after manually (might be it was supposed to be set like that in the first place) setting the following:

video_st->avg_frame_rate = (AVRational){ 90000, 90000/u8fps };  
av_stream_set_r_frame_rate(video_st, (AVRational){ 90000, 90000/u8fps });

where u8fps is the assumed rate of frames per second, and the 90000 is the standard sampling rate for video (90kHz tick) Video is playing smoothly.

Regards, Pawel.