This "feature" (not exclusive, BTW, to Windows) was the cause of my eventual loss of religion, something neither war nor an evil first wife had been able to effect. A GUI's main disadvantage over the CLI, IMO, is that it is going to do SOMETHING (mainly select something or execute something) when a left mouse click is detected. If I mistype something at the command line, the OS will most likely give me the equilvalent of "Duh, try again!"
It is, I think, a REALLY bad idea for the perpetrators of the GUI to enable it to, without any warning whatsoever, substitute a different dialog under your cursor just as your index finger is pressing that damned mouse button. There are occasions when the results are downright infuriating. And the presto chango trick can be almost as annoying when you just have your line of sight to information you wanted suddenly blocked by the odd popup. Hey, programmers, stick those damned things in a properly identified notification area -- and keep them there!
I believe the fix for this in Windows would be a million user march on Redmond -- said users to be equipped with Louisville Sluggers. This may not seem like a helpful suggestion, but I suspect that it is the only suggestion that might actually work.