To me the process of having to close the confirmation messages seems a bit too much. Sure, it's just one more click but that click tends to reload the page (not sure if by design or that event just isn't being caught via JS). Unless it's an error message I would like to be rewarded for sending information or adding to the site by NOT having to close another popup that congratulates me on doing it correctly.
For some reason, your system just doesn't want to allow me to check-in to Salt Lake City, UT without a confirmation ... even though I have been here, and checked-in here numerous times! Yuck! :-)
I can check-in in other cities without confirming ... Provo, UT this morning ... Park City, UT the other day ... but every single time I come to Salt Lake City, UT I am sent this silly confirmation message ... are you sure? Well yeah! I am! Just like last time, and the time before! :-)
Motivation: After a user signs up with an email address, they're sent a confirmation email. That's one more email that needs to make it past a spam blocker, and one more hassle during the signup process.
Feature: Check to see if the email they registered with matches the email associated with the activation code, and don't send them a confirm code if it does. In order to create a consistent user experience it's best to still send them an email letting the user know that they're registration process is complete for the login name used (a handy reminder if they later forget it).