I'm not sure what you mean. The configure.php files have the same perms as the other php files in the installation. They have the right contents. I don't believe they have to be writable by the webserver user, and they weren't on the old site which worked fine. The config in them has clearly affected the execution of zen cart, since SSL checkouts are working and the initial admin login gets redirected to secure.example.co.uk.

The file ownerships and permissions are identical on the two servers, set using the same script.

The only other difference relating to SSL between the two servers that I can think of is that on the old server the secure.example.co.uk domain and the www.example.co.uk domain were on separate IP addresses. On the new server they share an IP address.

If necessary I can set the new server up with 2 IP addresses too. I'll try it tomorrow if I haven't resolved this. However, I didn't think separate IPs would be necessary. Is there any way the IP addresses could affect the generation of these URLs? It sounds far-fetched...