I also have this issue, where half of my videos - converted with Kottori's Media Converter - are slightly out of sync, the sound being a fraction of a second ahead of the video. It's too bad because the video quality is terrific. I assume that if you edit the configuration file like that, you have to re-edit it all the time (depending on whether the video is out of sync and by how much). Bit of a hassle; obviously I concur with the suggestion to make it a feature inside MPlayer...