It seems like you may not be triggering the update on the user confirm page to make the userEmailVerified a 1.
When I look at the link closely I can see that you are missing a parameter, the link is:
After the ID=1 there should be a &code that is missing. The formatting that makes this is held in the Universal_Email > Templates > registration.php and verification.php. Have you made any edits to these pages? If so you should get them back to their original state to have them work. If you have not made any edits to these pages please post back with both of them attached to your reply in a zip archive so that I can take a look at them.
I will let you know what I discover. If I can't resolve it quickly for you I will open a ticket.