Well, I'm relatively certain that it isn't anything wrong with the encoding or mplayer, but one of my audio drivers seems messed up.

Whenever I played some of the offending video samples, depending on the audio family, I will hear quite a bit of weird feedback. I had this problem with the default audio driver (not sure how to check what this actually is) with an entire collection of episodes, so I switched to ffmpeg by using the -afm switch. I thought this fixed the problem, but there are still a few files where some distortion can be heard.

The interesting aspect of this is that VLC and Kaffeine both play the video files completely fine. I'm wondering if this is an issue with my encodes, or if VLC and Kaffeine just use different audio plug-ins.

Anyway, the whole thing is really just confusing me, and I'd really like to be able to use mplayer; I have a lot of custom inputs and everything, mplayer users probably understand.