It seems that if you have a username.github.com or orgname.github.com site created before the com-to-io switch that isn’t using the Automatic Page generator, turning on the Page generator creates an weird situation where changes to the *.github.com repo won’t change the site. It’s like the page generator creates an invisible *.github.io repo and ignores your changes to the *.github.com one.

I was trying to replace the Automatic Page Generator content on a Github site with a Jekyll install last week and it seemed to never update. I checked in the files into the master branch. Everything seemed correct but the site would not update. It would only show the old Page Generator content.

The original site was an Octopress site and the repo was created before Github switched to using .io for organisation and personal sites. So the repository was orgname.github.com. But sometime after the com-to-io switch the Automatic Page Generator had been used to replace the site.

On a hunch I renamed the repo to orgname.github.io and - boom! - it worked.