GitHub Pages has changed and they now prefill site.github with debug/config information. This can lead to breaking of your pages if you have decided to use this in your templates. Figure that I would run into this issue, in my case changing from site.github to site.githublink resolves my issue. But you may get caught out by this! Make sure you don't use that jekyll variable anywhere.
Changes are here ignore the one to the _post folder of course.