A client with IE9 has noticed that when using lightbox or Fancybox (in a WebYep site) and then having the image popup over the page, if an embedded google movie is positioned close by the popup image and/or overlay appears behind the embedded google movie
To the movie embed code makes no difference. The lightbox or fancy box popup and/or any overlay appears “behind” the static movie holding pic in IE9 ~ testing in an old IE6 box works ok, looks like IE9 has made a set backwards.
A very quick search shows there were some known bugs with IE9 and Lightbox which may, in part, contribute to your problem. From what I’ve seen there doesn’t seem to be a workaround, short of changing the movie format, though I haven’t looked thoroughly so don’t take that as an absolute.