I tried the same video with a different transcoder, Konttori's Media Converter (v2.02). Unfortunately I found out afterwards that it defaults to the same codec (3ivx D4 4.5.1 -- what are the odds, eh?) and with the same result: Around minute 13 of a 25 minute video frames start dropping and audio gets ever so slightly choppy (the audio is a lot less annoying than the video, but it's definitely there).

Now, in fairness, this is a Penn&Teller ******** video, so it might just be that mplayer doesn't like the gratuitous swearing and rampantly unfunctional nudity. Still, I like it and I really wanna watch it, even if "jerkiness" gets a totally new meaning with boobs in the picture.