I had a problem with this here Jekyll install/ blog in that I couldn’t get the CSS to render and nearly abandoned Jekyll because it was the third major issue I’d encountered in the few short weeks of trying to get it going. Thankfully a guy named Gungor on the Jekyll Gitter forum pointed out to me that my css was being served at http while my site was at https (It’s possible that I have those reversed). I spent the next three hours trying to figure out what I needed to change and, after trying every iteration of http/s in the url and baseurl variables in my _config.yml file, I finally commented them both out and it suddenly worked. I wish I could explain why but if you’re running Jekyll on GitHub Pages with a custom domain see if that doesn’t fix your problem.