Are you using a non-square pixel ratio comp with PAR correction on? On the bottom of the Comp window is a little rectangle button with a double ended arrow over it, if it's checked on that could be your problem. When you have it checked the video will appear in normal aspect, but it will have little jaggies. If that doesn't help try posting a screenshot.
Jeff McBride
Motion Graphic Designer/Editor
LimeGreen
Chicago, ILwww.limegreenproductions.com