Could you share with us what website you are browsing, so that we can try and reproduce what you are seeing on our end? I've gone to popuptest.com, and it blocked most of the pop-ups there.
Also, some websites work a bit better using the mobile version of the website. You could give that a shot too.
If you go into the Internet Explorer for Xbox 360 Settings, make sure that you have "Turn on SmartScreen Filter..." checked, also "Use web pages formatted for mobile devices" checked. You can get to Settings in the browser by hitting 'Y' to open the Web Hub, then putting your pointer over the 'gear' in the upper-right corner.
Let us know if those things help. Thanks!