P.s. I just noticed that at the bottom of the original modules/create_account php there are 2 lines that are not included in the modules/custom/create_account php these are.

PHP Code:
if (!isset($email_format)) $email_format = (ACCOUNT_EMAIL_PREFERENCE == '1' ? 'HTML' : 'TEXT');
  if (!isset($newsletter))   $newsletter = (ACCOUNT_NEWSLETTER_STATUS == '1' ? false : true); 
Would they affect what comes out in the welcome emails ? maybe someone who knows a bit about Captcha may be able to tell me why this is not in the custom file ? and does it need to be ?