Well after 30 minutes of thinking I was going insane I have discovered that Apache will assume that redirects are for the http version of a site unless they are also stated in the SSL configuration for the site, this is due to the SSL part of the site is usually a virtual host with it’s own configuration.

The solution, to help me keep my sanity, was to create a seperate rewrite.conf file in the conf.d directory (which is automatically included in the default httpd.conf in Red Hat Enterprise Linux). This file can then also be included in the https configuration. i.e.

include conf.d/rewrite.conf