Further to the above I went through and replaced the following files from a fresh download of 1.3.9h and the problem is still there, I have no idea where to start looking.

/includes/modules/pages/create_account/header_php.php
/includes/modules/pages/create_account/jscript_addr_pulldowns.php
/includes/modules/pages/create_account/jscript_form_check.php
/includes/modules/pages/create_account/on_load_main.js
/includes/languages/english/create_account.php
/includes/templates/template_default/templates/tpl_create_account_default.php

I also checked the template files with WinMerge using a previous backup before the move and they are all the same. Everything was working until 2 days ago.