I really don't know :)
And whooami - it is my understanding that placing the flash in a div with a z-index doesn't matter in the least. Flash is out of the DOM scope, and therefore not really part of the HTML - it's an object that has it's own "policies" if you will. You can z-index it to hell, and it won't budge from the top. It's the param tag editing that does the trick - if you don't have that, then nothing will work. Also, the need for the line in the embed tag is necessary in some browsers (I can't remember which ones off the top of my head, though.)
Again, this is my understanding of how CSS related to objects like Flash, Quicktime and other such things, so don't take my word as gospel on the fact. But if you know otherwise, I'd love to see some links to that info!
Oh, and Eric - what whooami said about changing your plugin. Normally, you'd just edit it right there in the param/embed tags - but if the theme uses a plugin for it, save yourself some future headaches and just do it there :)