This is a common problem in browsers like IE where YouTube uses an older Flash-based version of its video player. It happens because, by default, Flash doesn't respect the CSS z-index property which defines which element is layered on top of each. So Flash objects appear on the very top.
To enable layering, "wmode" parameter with either "transparent" or "opaque" value must be added to video's OBJECT tag as described here.
If IFRAME-based embed code is used, you have no direct access to the OBJECT tag, but you can add "?wmode=transparent" to the end of video URL to instruct YouTube to add the parameter as described here. If the URL already has some parameters after "?" then add "&wmode=transparent").
<iframe width="440" height="253" src="http://www.youtube.com/embed/12345abcde?wmode=transparent" frameborder="0" allowfullscreen></iframe>
Article ID: 99
Category: 1-Minute List Builder