persisting problem

I was refered here from the spyware specific forum. I had been infected with the bestfriends virus. i did everything in the tutorial and my hijackthis log is clean. however, the problem i am having still persists. When a new window is opened in Internet Explorer, or even if I changed pages my pop-up blocker bar says it is blocking active content that could access my computer. I have switched to Mozilla Firefox for a browser now, but it worries me that the problem still exists on my computer. any suggestions?