If you have ever tried to place a div or similar HTML element on top of a swf flash object you will know that it always tries to take precedence.

You will need to do the following:

In the code for the flash add:

<param name=”wmode” value=”transparent”>

and in the embed area add:

wmode=”transparent”

If you are using SWFObject to insert swf files you can do the following:

<script type="text/javascript">
var so = new SWFObject("movie.swf", "mymovie", "400", "100%", "8", "#336699");
so.addParam("wmode", "transparent");
so.write("flashcontent");
</script>