I had the same issue and this is my solution:
var fixZindex = function(){
$(".oembed").css('z-index','1').css('position','relative');
$("object").css('z-index','1').css('position','relative');
$("embed").css('z-index','1').css('position','relative');
var elements = document.getElementsByTagName('embed');
for(var i=0; i< elements.length; i++){
elements[i].setAttribute("wmode","transparent");
var para = document.createElement("param");
para.setAttribute("name","wmode");
para.setAttribute("value","transparent");
elements[i].parentNode.appendChild(para)
}
}
$(document).ready(function() {
$(".oembed").oembed(null,
{
embedMethod: "append",
maxWidth: 500
});
setTimeout('fixZindex()',1000);
});
I apologize for the mix of js/jquery. I'm not a jquery expert by any means so if someone can recode that solution in straight jquery that'd be rad.