I have been using the ThickBox plugin for WordPress on my site for a while now. When you click on a link, the images are shown in their own window with a darkened background. This worked great until I put together something on another of my photography sites here. At the top is a flash movie (yes, I know I don’t like having a flash movie, I will move on to HTML5 video when I can) and at the bottom are images. When you click on the images you get the same lightbox effect as the plugin. The only trouble was, it was pointed out to me that in IE, the video stayed on top. Oops.
A little searching the internet found the solution. Check out here for the fix, and here for some background on how it works and for other options you have. It is now working as expected. Thanks Steve for pointing that out to me.