Revisá tu código de incrustación. Esto funciona sin problemas:
Código PHP:
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
<title>Documento sin título</title>
<script>
function changeFlash(url){
var d=document;
(window.ActiveXObject)? d.getElementById("flashMov1").movie = url :
d.embeds["flashMov2"].src = url;
}
</script>
</head>
<body>
<object id="flashMov1" classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" width="320" height="303"><param name="movie" value="http://eplayer.clipsyndicate.com/cs_api/get_swf/2/&csEnv=p&va_id=879953&wpid=311&cpt=8"></param><param name="allowfullscreen" value="true">
<param name="allowscriptaccess" value="always" />
</param><embed name="flashMov2" src="http://eplayer.clipsyndicate.com/cs_api/get_swf/2/&csEnv=p&va_id=879953&wpid=311&cpt=8" width="320" height="303" type="application/x-shockwave-flash" allowfullscreen="true" movie="http://eplayer.clipsyndicate.com/cs_api/get_swf/2/&csEnv=p&wpid=311&va_id=798398&cpt=8" allowscriptaccess="always"></embed></object>
<br />
<a href="#" onclick="changeFlash("http://eplayer.clipsyndicate.com/cs_api/get_swf/2/&csEnv=p&va_id=879936&wpid=311&cpt=8")">CAMBIAR</a>
</body>
</html>