The problem is seen well when you get video file information with ffmpeg:
I have found a pretty helpful article for ffmpeg recompile: http://fozzolog.fozzilinymoo.org/tech/2009/11/recompiling-ffmpeg-for-fedora-12-to-add-faac-support.html . However, it looks like the instructions were incomplete.
I could not get it compiled in a sane manner in Fedora 11. However, one can get it now from atrpms.
When you need to capture something from your screen, there is a great program which does the job for you, xvidcap.
“LiVES is a simple to use, yet powerful video editor and VJ tool.” Written at http://www.gnomefiles.org/app.php?soft_id=432. It is claimed to be capable of handling a variety of file formats.