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:
[code lang=”javascript”][/code]

and in the embed area add:
[code lang=”javascript”]wmode=”transparent”[/code]

If you are using SWFObject to insert swf files you can do the following:
[code lang=”javascript”]