Dave, It’s dead simple. FFmpeg developers do not care about you - or anyone else. The only thing they care about is sitting in a cave admiring their awesomeness.
I’d suggest you go and file a bug with VXL and tell them that their ffmpeg handling is wrong (as they linked to and not forked it). While doing this, suggest to them that they might wanna use GStreamer (or Xine or whatever) instead, as those projects provide stable API and are actually more powerful.
In Swfdec I’ve seen the light and removed the ffmpeg option. They don’t care about me, so I won’t care about them.
Or to paraphrase: There’s always the ffmpeg solution to every multimedia problem — neat, plausible and wrong. Or did you pad and align your buffers?