Te envío mi código que ha funcionado, capa.swf es un cuadrado amarillo de 550 y 400. IMPORTANTE debes poner el flash tranparente (wmode):
<html>
<head>
<style>
#delante{
position:absolute;
z-index:200;
left:112px;
}
#detras{
position:absolute;
z-index:100;
}
</style>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<title>Documento sin título</title>
<script src="Scripts/AC_RunActiveContent.js" type="text/javascript"></script>
</head>
<body>
<div id="delante">
Espero que funcione
</div>
<div id="detras">
Espero que funcione
<script type="text/javascript">
AC_FL_RunContent( 'codebase','http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=7,0,19,0','width','550','heigh t','400','src','capa','quality','high','pluginspag e','http://www.macromedia.com/go/getflashplayer','wmode','transparent','movie','cap a' ); //end AC code
</script><noscript><object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=7,0,19,0" width="550" height="400">
<param name="movie" value="capa.swf" />
<param name="quality" value="high" />
<param name="wmode" value="transparent" />
<embed src="capa.swf" width="550" height="400" quality="high" pluginspage="http://www.macromedia.com/go/getflashplayer" type="application/x-shockwave-flash" wmode="transparent"></embed>
</object>
</noscript>
</div>
</body>
</html>