You must set the wmode parameter of the Flash object when embedding in SWFObject.
Here is a short tutorial for this.
Here is the modified code for your problem:
<script type="text/javascript"> swfobject.embedSWF("index.swf", "my_flash", "100%", "100%", "8.0.0", null, { wmode: "transparent" }); swffit.fit("my_flash",900,650); </script>
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