Carsten, I'm on Kubuntu 10.04 and I had the same problem.
As you also found out, official builds work well.
I also fixed the problem with my builds though. I compiled FFMPEG 0.8 (without
any additional libraries, which doesn't seem to really affect the encoding or
decoding capabilities) and I pointed the scons compiler to my ffmpeg build.
Everything works great now, no jagged edges anymore.
For compiling ffmpeg, I configured it with the --prefix="/opt/ffmpeg" option
so that it didn't overwrite the system's ffmpeg version. As blender didn't like
the full library compilation of ffmpeg (with x264, direc, etc etc) I just
compiled 2 different instances of ffmpeg, one for standalone usage with all the
codecs, and another one with no extra stuff for blender.
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