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Assuming you have made all assets on the final frame transparent (or removed them altogether) and placed a stop(); action in the timeline then what you are seeing is the background colour for the Flash file as specified in your HTML.
Make it the same colour as the surrounding background in your HTML.
Object: param name="bgcolor" value="#ffffff"
Embed: bgcolor="#ffffff"
...
<object width="550" height="400">
<param name="movie" value="file.swf">
<param name="wmode" value="transparent">
<embed src="file.swf" width="550" height="400" wmode="transparent"></embed>
</object>
Using SWFObject (better,)
<script src="swfobject.js" type="text/javascript"></script>
<script type="text/javascript">
var myvideo = new SWFObject('file.swf', 'flash-obj-id', '550', '400', '6', '#ffffff');
flash-obj-id.addParam("wmode", "transparent");
window.onload = function() {
if (document.getElementById('document-obj-id')) { flash-obj-id.write('document-obj-id'); }
};
</script>
Transparent works out better in the long run, because unless you are using web-safe colors, you will see some differences in how various browsers and Flash interpolate the same color assignments. Sometimes the same assignment color will shift between the browser and Flash.