If you use SWFObject , you'll probably get rid of this problem. This is the recommended way to insert Flash objects into HTML, and is required if you want the SWF and JavaScript to pass information back and forth. You have 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