Prueba agregando el param
wmode a
transparent Código PHP:
<script type="text/javascript">
// <![CDATA[
var oSWF = new SWFObject(...........................);
oSWF.addParam("scale", "noscale");
oSWF.addParam("wmode", "transparent");
oSWF.write(..............);
// ]]>
</script>