Not sure exactly what may be going on.
Is the "simple_6_transcode_opaque - async - ffmpeg" transcode sample working ok? If that is the case, please compare it to the src code you are using for just encode + muxing, there may be some slight differences, requiring updates.
Also, it is possible, that if you are using a recent release of the FFmpeg binaries the FFmpeg APIs may have changed since the creation of this sample, thus resulting in some incompatibility.
Based on your description I do not understand your setup. You refer to two different samples, (1) the transcode sample "simple_6_transcode_opaque - async - ffmpeg" part of the Media SDK tutorial, and (2) the quite old encode sample code that was part of Media SDK muxing with FFmpeg white paper.
The code reference "FFmpeg_Reader_Init" is part of (1) but the line number you refer to is not corresponding to the tutorial sample code which leads me to believe you are using your own modified code.
Note that (1) is a transcode sample and the call to avformat_find_stream_info() in FFmpeg_Reader_Init() is used to parse a media container not a raw YUV file.
Then in your post you abruptly refer to a command line which corresponds to the encode sample (2) ?