Installing ffmpeg from original source:

Clone the github repository: https://github.com/FFmpeg/FFmpeg
# patching ffmpeg. See patch file under you MediaMosa installation: site/all/modules/mediamosa/patch
cd ffmpeg/
./configure --enable-nonfree --enable-libx264 --enable-gpl --enable-pthreads --enable-libmp3lame --enable-libfaac --enable-libvorbis --enable-libtheora --enable-libgsm --enable-libxvid  --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-version3 --enable-x11grab --enable-libvpx --enable-pic --enable-libxavs
make
make install
cd ..

Or use this github version, this has already been patched:

Clone the github repository: https://github.com/www-madcap-nl/ffmpeg
cd ffmpeg/
./configure --enable-nonfree --enable-libx264 --enable-gpl --enable-pthreads --enable-libmp3lame --enable-libfaac --enable-libvorbis --enable-libtheora --enable-libgsm --enable-libxvid  --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-version3 --enable-x11grab --enable-libvpx --enable-pic --enable-libxavs
make
make install
cd ..