I just tried again the plugin and confirmed that it's working as how it should.
Can you perhaps send a link to your site so i can try to register there?
Also, just to make everything clear this is how the plugin works.
1.] User will register (like they normally do)
2.] The user will received an email with their confirmation link
3.] When the user click the confirmation link, they will received the password on their email.
The confirmation link is directed to the wp-login.php. To be exact it will redirect the users to http://yourwebsite.com/wp-login.php/?action=confirm&eckey=XXXXXX where the XXXXX is a randomly generated string.