I am adding muxing to my video player and I am running into a wall.

If I use mp3 (libmp3lame) as the audio encoding method, the resulting file has perfect audio that ends up short (like 256 frames). If I use PCM_S16LE, the audio is complete albeit I end up with some stutters in the audio (probably because of some bad use of swresample or the fact that my viewer splits audio into frames upon reading them).
I cannot reproduce the problem with muxing.c on which my code is based.
I can show the source code albeit it is a tad long.

If anyone can think of something to try, I'm all ears.
Thanks in advance.
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