I'm not sure how much this affects people who use the taskbar at the bottom of the screen because I have never used it there on any Windows OS, but especially in Windows 7 some windows open under the taskbar (this may have happened sometimes in Vista but if so is definitely much worse in Windows 7).
As you'll see in the example, I always turn on my "desktop" toolbar [by the way, possibly the most under-appreciated good features of the taskbar] and set the taskbar wide enough to show three columns of icons.
The "Run" pop under in this example isn't the worst I've seen but it's an easy one to remember.
Does anybody know of a setting to "fix" this issue or is this simply a Microsoft bug to be fixed?
Note on attachment: Because this snapshot was taken on a portrait mode monitor it is quite tall. You will likely need to click on the image twice or three times to get your browser to display it full size.