Some of you might be aware that 1.5 years ago some of the ffmpeg devs forked ffmpeg and continued to work on their controversial fork called libav.
What I didn't realise is that there is actually one major distro using this libav fork rather than ffmpeg, despite there are numerous technical reasons why the libav fork is inferior to ffmpeg.
That distro is Debian, hence also Ubuntu has been using libav since 11.04 (as far as I could find out).
I just came across the follwoing article that explains why this is a bad idea (i.e. Debian and Ubuntu users have to make do with a technically inferior library):
Some quotes that explain what the problem with libav is:
Michael [the primary ffmpeg dev] also started to merge the Libav changes back into FFmpeg every 1-2 day, with a lot of forgotten, previously rejected, sometimes controversial features, or in stand-by such as ffmpeg-mt.
Libav is totally ignoring FFmpeg since the beginning (almost 2 years of development now). And this is of course not only related to features, they also don't give a damn about regressions they introduce, security issues (look for "j00ru" in the FFmpeg history for instance), and overall bug fixes. This is not 3-4 patches, there are hundreds of them.
At times, you can see them picking random stuff from FFmpeg, but they often re-fix them in their own way
In other words, while ffmpeg contains everything that libav contains, the other way round is not the case. Libav is missing a lot of stuff (features and bugfixes) that's only in ffmpeg.
This is just meant as a 'heads up' to all Debian and Ubuntu users, if you encounter problems related to ffmpeg/libav it's likely because Debian/Ubuntu is using the inferior libav rather than the original ffmpeg.
I'm not sure what the solution for you is: I don't know if you can just build ffmpeg and swap out the library binaries, I somehow doubt it and think you would likely have to rebuild the apps that use ffmpeg/libav too (which would be a lot of hassle).