The code is definitely there in the template pages. I did a test on your site and registered a new user, first name WA last name Test. I got the verification link in the email and can see that the code parameter is there like it should be.
When I clicked on this link it took me to your confirmation page and it told me my email had been verified.
Take a look at this user's record in your db and check the UserEmailVerified column. If it is not set to 1 please post back with a copy of your users_Confirm.php page. I will do a quick check to see if I can spot a problem and if not a ticket will be opened.