function my_oembed_wmode( $embed ) {
	if ( strpos( $embed, '<param' ) !== false ) {
		$embed = str_replace( '<embed', '<embed wmode="transparent" ', $embed );
		$embed = preg_replace( '/param>/', 'param><param name="wmode" value="transparent" />', $embed, 1);
	}
	
	return $embed;
}
add_filter( 'embed_oembed_html', 'my_oembed_wmode', 1 );