If my understanding is correct, browsers stop when they come to link and script tags, download the files, then continue processing. That would mean that the base tag isn't taken into account until after your css and js files have been requested. You might want to try putting the base tag immediately following the meta tags, before any link or script tags.
And with HTML5 doctype, you shouldn't have the self-closure in the base tag.
☆ A M B ☆
