Open the System Preferences and click on the Users & Groups icon. Choose your account and click on the Login Items tab. Is there anything in there you don't recognize (don't start dumping items unless you know for sure they shouldn't be there).
Does the popup start as soon as you turn your computer on or restart? If so, I would then indeed suspect some type of startup item has been installed. Did you install any new software the other day? If so, what was the source? Questionable, illegal sharing site, legitimate?
A quick check to see if it's related directly to your current user account. Create a new user account and log in to that. If the popup is gone, then it's related to something in your normal account. If the popup occurs there, too, then it's something that got installed in either the System or root Library folder.