Yes, unfortunately I had to enable pop-ups for registered users. However, you should only get one pop-up per visit. If they bother you, you can disable them in My GTPlanet "User Options".
Ad revenues keep going down due to the spread of ad blocking software, and there has to be so much money to keep the backend infrastructure up and running. Introducing pop-ups and contextual links is an attempt to keep revenue at a normal level.