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 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>