Hi Corey!
In the SSC there is a section called "Client Administrator only options" where you can set up the number of days after you get a warning. Check the value to see how big it is, maybe it's set to 1 or 2 and that is why after a couple of days of not updating it shows you the pop up.
I have seen it ofter times in people that have been on holidays for a while or laptops that don't update regularly. However, once they connect to the server they will receive the updates (the pop up is triggered at user logon). That's maybe why you are seeing the pop ups but when you check the defs are up to date.
I hope that helps ;-)