I was trying to open fancybox ontop of a page with a flash player. The border and sometimes all the iframe was being displayed beneath the flash player in Internet Explorer, making it very ugly and impossible to use. Setting z-index to the flash player did not work.
Wrap the flash player in a divider and add styling “z-index: 0” to the container and add an extra parameter to the flash player “wmode” with value “transparent”.
<div style=”z-index: 0;”>