after the security assist wizard creates the pages, it opens the access pages manager window for you to apply access restriction to the pages in your site.
the only way the access rule would have been applied to the connection file is if you selected the connection file in the access pages manager.
for the registration page, it is missing the following code at line 1:
<?php require_once( "../webassist/security_assist/helper_php.php" ); ?>
the login page is showing validation errors because some of the spry assets files are missing from the server, for example: