I've been working alot on the Gnome Mplayer issues with subtitles. Now I have to admit that most of what I know about subtitles and mplayer, I've learned in the last couple of weeks. I do know that a current version of mplayer is needed for proper subtitle support. So if subtitles are not working right, then get a newer version of mplayer. I've been testing with mplayer SVN (Mar 25,2008) and everything is working pretty good. You can even switch subtitles while the video is playing back.