I have found a workaround (more of a fix) for this problem. I thought that I should post it here for your information and others.

The first thing that I tried to do was put a div container around the flash object and use CSS to set its position and z-index. This didn't work. After much searching and more reading, I ran across someone with a solution. It is a general Flash solution for layering HTML and Flash content. (link: http://joshuaink.com/blog/82/flash-content-and-z-index)

First, wrap your flash content in a div container with id="flash" or whatever name you want. Then make sure that you add <param name="wmode" value="transparent">to your object tag. Also make sure to set wmode="transparent" in the embed tag.

Now, use css to set the position and z-index for your div. —> #flash { position: relative; z-index: 0; }
Don't set negative z-index values. It will make your Flash disappear.

CSS Part:

#flash {
  position: relative; /*or absolute*/
  z-index: 0;
}

HTML Part:

<div id="flash">
  <object .... >
    <param name="wmode" value="transparent">
    <embed .... wmode="transparent">
  </object>
</div>

That's it! Your Flash content will now behave and let the menu show up on top. Have tested in Firefox 1.0.x and IE 6/Win. Will soon test in Safari, Firefox for Mac, Camino, and IE for Mac. I will post to let you know their support.

Hope this helps someone other than me.