More information is needed - are you saying the entire application isn't rendering when you're running in a browser? Does the Flash player display appear at all? (Right click to see the context menu available to verify.) Is this after you deploy the application or just when you are starting the application directly from Flex Builder? Did you alter or remove any files in your project's html-template folder?
If you're talking about after you've deployed to a server, and you're not even getting a Flash player view in your browser (when you right click it would say 'About Adobe Flash Player'.. at the bottom of the menu), something is probably wrong with your html template. It could also be something wrong with your build process (are you using Ant?)