I had some problems in the past with mencoder's Xvid 2-pass encoding where it would constantly overshoot the specified bitrate (see here and here). I remembered today that I had some stuff installed in /usr/bin/, either from a previous ffmpegX installation or some other thing I had installed. I deleted mencoder, mpeg2enc and some other stuff that seemed to be ffmpegX-related, then I installed 0.0.9u and everything works like it should again!