Thank you for putting in so much effort to get this worked out. I have checked the helper files myself and can see that they differ. What seems odd to me is that the helper file that comes from Security Assist should be the updated version.
To help get to the bottom of this I have opened a ticket for you. To check the status of the ticket or update it please visit your support history:
The version of the Security Assist > Helper_PHP.php file that comes in the User Registration Solution Pack and the version of this file that comes from Security Assist 1.1.8 differ. This causes the check for verified email to falsely show that the user has verified their email when this is not the case if using the version of this file that is generated by Security Assist.
make sure to use the version of this file that is included with the User Registration Solution Pack.