I think in the next update, when you select the Online Help and the Check for updates now... links it really should be opened up in a new window, rather than go over an existing one.
Not to disagree with you but your supposed to have your browsers closed when you use CCleaner. So it shouldnt matter if it goes over an existing window.
What, just to have a look at the links? But, you can just uncheck reuse windows for launching shortcuts in IE options. So case closed!