Finally I got the layout working. The problem being an incorrect setting of url: on the _config.yml file:

url: "http://bjacquet.github.io/" # the base hostname & protocol for your site

That forward slash at the end was causing an incorrect path for the css files and all other hrefs. Only when I looked at the html source code that I notice the horror!

<link rel="stylesheet" href="http://bjacquet.github.com//css/main.css">