Before the ActiveX patch came out that changed how IE displays Flash and other objects, Microsoft wrote how the browser would behave differently. When I installed the fix, my browser does not display the prompt.

Instead it outlines the object when moused over and displays a tool tip that states "Click to activate control." This is far less annoying and, as far as I'm concerned, acceptable. I'm glad it's not the other way, but why wouldn't they describe the effect correctly?

ADDED 5/18/2006:
I experienced this pop-up today for the first time on a page with a Shockwave object and a page with QuickTime.