If anyone is having this issue, it may have to do with the email headers when sending the new user confirmation email. This is when using SMTP to send email. The From header domain needs to match the host domain or the from email needs to be allowed(as in Amazon SES).
in the file /public/class-wp-custom-register-login-public.php around line 333 and line 503, change
$headers[] = 'From:' . get_option('blogname');
to
$headers[] = 'From:' . get_option('admin_email');
or best change them both to
$headers[] = 'From:' . get_option('blogname') . ' <' . get_option('admin_email') . '>';
or simply remove the additional email headers altogether because most smtp email plugins will handle this automatically.
