If you use the Swfobject, You’ll probably get rid of that problem. It is the recommended way to insert Flash objects into HTML, and is required if you want SWF and Javascript to be able to pass information back and forth. Has a embed code generator on the project website.
<html>
<head>
<title>Usando SWFObject</title>
<style>
body {background-color:#c00;}
</style>
<script type="text/javascript" src="//cdnjs.cloudflare.com/ajax/libs/swfobject/2.2/swfobject.js"></script>
<script type="text/javascript">
// Embed normal
var flashvars = {};
var params = {};
params.quality = "best";
params.wmode = "transparent";
var attributes = {};
swfobject.embedSWF("SEU-SWF.swf", "myAlternativeContent", "800", "600", "9.0.0", false, flashvars, params, attributes);
// Embed de YouTube
// https://developers.google.com/youtube/js_api_reference#Embedding
var yt_params = { allowScriptAccess: "always" };
var yt_atts = { id: "myytplayer" };
swfobject.embedSWF(
"http://www.youtube.com/v/aZMbTFNp4wI?enablejsapi=1&playerapiid=ytplayer&version=3",
"ytapiplayer",
"425",
"356",
"8",
null,
null,
yt_params,
yt_atts
);
</script>
</head>
<body>
<div id="myAlternativeContent">
<a href="http://www.adobe.com/go/getflashplayer">
<img src="http://www.adobe.com/images/shared/download_buttons/get_flash_player.gif" alt="Get Adobe Flash player" />
</a>
</div>
<div id="ytapiplayer">
You need Flash player 8+ and JavaScript enabled to view this video.
</div>
</body>
</html>
Jsfiddle
Actually, your question has a problem because you do not show the full code. The above example is invalid.
– brasofilo