If for some reason, in my case I had duplicated a Site Definition in the Site Manager and changed the URL (for a new version of the site, not in version control for the time being) updating the templates no longer updates the pages created from that template throughout the Site.

If this is the case then you may need to disable the Site Cache by going into the Site Definition for that Site and deselecting Enable Cache. Save and update the template, then you should be prompted to update. Once this is done check that your pages are being updated correctly, then you can re-enable the Site Cache if you wish.