When I run jekyll --server my site is available at http://localhost:4000/, but when I deploy to GitHub Project Pages, it\'s available at http
I use jekyll-bootstrap and deploy locally on port 4000, but my github pages url is user.github.com...i think that it depends on how you originally create the repo. Originally I used the auto page builder that github offers which created the repo in a very wizard like manner.
I just followed the steps at:
http://jekyllbootstrap.com/
Hope that helps