Thanks!
I upgraded ffmpeg to v1.0, avbin to the latest, and pyglet down to latest stable. Didn't seem to affect much, but I do think I get less data corruption problems with bad audio packets.
Ultimately, I found a format that "just works". I'm just converting everything to that format.
After building ffmpeg with --enable-libx264 and --enable-gpl:
cmd = '''ffmpeg -i \"%s\" -strict experimental -vcodec libx264 -vprofile high \\
-preset slow -b:v 5000k -maxrate 5000k -bufsize 5000k -acodec ac3 \"%s\"''' % (in_video, out_video)
does the trick.