Lately I've been having the same problem across multiple browsers and multiple WP blogs (all running 3.1.3 or 3.1.2) with the auto-embed/oEmbed functionality. Any YouTube video that's embedded this way is displayed at a size that is just slightly too wide. This results in thin black bars on the left and right of the video, and happens with videos that are 16:9 or 4:3 aspect ratio.
Examples can be seen here: http://www.canopyco.com/blog/
Even when using the [embed] shortcode and specifying a width and height, that only defines the maximum width & height and still automatically sizes the video. I'm not sure if this is a YouTube/oEmbed problem or a WP problem.
Anyone else experiencing this? Anyone have a fix?