Jekyll Bootstrap is a really wonderful toolkit to bring-up Jekyll in github. I had suffered this issue for long time, until I found the introduction of it here: (http://www.yangzhiping.com/tech/github.html)
I had a try immediately, and it's ammazing!
Yeah, I will put my blog or technical collections here :-)
note: after some study, seems octopress is better? see (http://blog.kitchen.io/archive/2012/08/19/jekyll-bootstrap-and-octopress/)