In order to have HTML elements on top of Flash movies, you need to include the parameter - wmode="transparent"- in your <embed> element. We use HTML elements for our dropdown menus and we generally want them on top of any content on the page.
If you also have an <object> element, you can add <param name="wmode" value="transparent" /> inside that element.
For wmode to work properly in both IE and FF an attribute should be in both a <param> and the <embed> tag.
For example:
<PARAM NAME="wmode" VALUE="transparent">
<embed wmode="transparent" src="flash/hello.swf">