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I'm not sure if that background is in the flash or not. If it is, there isn't anything you can do about it outside of Flash. If you have access to the .fla, you can simply remove whatever graphic/drawing is creating that color.
If it isn't in the Flash, you can pass a parameter to set either the background color to the brown or the wmode to transparent.
http://kb.adobe.com/selfservice/view...rnalId=tn_4150
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I am not a flash guru, but I get the white box in every browser, and it looks like it's part of the flash movie. (if you right click it you get the controls) Once the pre-loader script dwindles out, it seems to go away, so I would look into your pre-loader.
I think if change the background of your pre-loader/progess bar to transparent and I'll bet money it goes away.
