This is not a problem, that's a specific configuration of some DVDs, it happens beucause some DVDs to fit in a 4:3 (fullscreen) TVs put the black borders on the top and botton. When you try to view these movies in a widescreen there will be black borders on the right and left because the format with the original top and botton border is 640 x480 (4:3).
To fix that you just have to select the Otion "Video Zoom" from the Apple DVD Player menu "Window":
There you can strech the movie the way you like to fill your widescreen.