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You didn't mention the html file your swf is embedded into--did you try checking the size of the application there? Check it carefully--I think there's a width/height setting in two different places, for different browsers? These kinds of screen resolution issues can be a pain, sometimes.
I had not thought about that, but even when I generate a test app from within Flex it still happens. I will check the html flash callouts but I don't think that is my problem, it looks good at 1024x768 but only get about 1/2 on the new and improved ie8. But thanks again for reminding me of the html component in all this there may be an opportunity to tweek that one day.
Specifying height and width in the Application tag will give the absolute size of the swf file. You can double check it by double clicking on the swf file in the file system. It will display in Flash Projector.
I faced same issues & resolved by making widths & heights for containers in % <mx:VBox width="100%" />