I searched several terms and didn't find anything... so please forgive me if this is already answered.

This has to do with the classic case of embedded objects being placed at the top layer, which will cover any dynamic (in my case javascript) drop-down menus on the page.

What parameter do you use with the unity embed to prevent this?

For the Flash Player, wmode=opaque has usually done the trick for me.

No, unfortunately this isn't available in Unity. The reason being, Unity content is rendered on top of everything else by the user's graphics card, which makes it impossible for any other web page elements to render on top of it, or for any other items on the page to be visible "through" it using transparency.

I have the same problem with unity and drop-down menu that is hidden behind the unity. It works well on Fire-Fox but on chrome and IE the problem occurs.