May or may not be related – I’m also on 3.0.3 and using S3, mine has uploaded all of the theme files to Amazon but never replaces the URL for them when you load the page.
For example, if you view the background image it is still shown as https://www.mysite.com/image.png instead of static.mysite.com/image.png – however, the images in the posts are on the CDN. If you manually change the URL in the address bar from www to static then the file is there. Clearing the cache etc does nothing.
Everything seems to work except possibly the URL replacement…?