I too have been having this problem. I have two different computers, both running Windows 7, one computer was from Dell with Windows 7 installed, the other, I did a clean install on the existing computer. The new computer from Dell does NOT have an issue with popups. The clean install on the existing computer, DOES have issues with popups. Continuous issues. When I launch the manage popups, in Chrome under the hood, network/change proxy settings, it launches IE security. There is no option to manage popups within Google.
I am running 14.0.835.202 m and when I check for updates, it says I am running the latest version.
Not sure if this helps, however, if there is not a fix shortly, I will be moving off Chrome. It is annoying to have something as basic as pop up blocker not working.