The info in your post doesn't give me enough to answer your question... So lemme ask a few of you.
1. When you say "a little box" pops up, are you talking about in your web browser? Are you browsing the web when this happens? Browsing a network share? Doing something else?
2. If it's when you're surfing the web, is it a pop-up browser window with an HTML form? Or is it a basic authentication dialog like this one:
If it's a dialog like this one, then your school is using basic authentication, and the server has a limit (timeout) on how long you can go before you have to log in again. If it's some kind of form-based login, then it's storing your session in a cookie, and that session is timing out (probably on the server, possibly by setting the expiration on the cookie.) If it's some kind of other app that you're logging into, then you'll have to explain your situation some more. No matter what it is, my informed opinion is that the system administrators have decided to force users to log in occasionally as a security measure (to prevent your roomate or the guy down the hall from logging in and sending gay porn to your physics teacher.