The most annoying problem with Internet Explorer while browsing some web pages containing interactive Flash animations is "Click to Activate and use the control" message.
When Microsoft updated Internet Explorer in 2006, they introduced this problem (yeah..they introduced this problem because of license issues) which requires uses to explicitly click and activate certain controls before using them.
The good news is Microsoft IE blog has announced that this problem will be soon corrected. The software update to Internet Explorer is expected sometime during December 2007 through Vista SP1, Windows XP SP3 and Microsoft Download Center.
It's quite interesting to observe the corrective measures taken up Microsoft IE team after loosing major browser market share to Google supported Firefox. Few weeks ago Microsoft removed Windows Genuine Advantage Check before installing Internet Explore 7.0 which allowed all the pirated windows users to enjoy tabbed browsing of IE 7.0. Looks like Microsoft is working around the clock the regain the web browser market share.