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When I had Vista (which lasted three years), certain system tray icons would sometimes not appear even though they were running okay. I found a number of threads of other people with the same problem. You can set these up in properties, I know, but they would act erratically.
Now that I've had Windows 7 for six months, it's only happened once. Today the icon for the video card didn't show up, but there was a blank area where it's supposed to. In fact I could still right click on that area to start the video card setup screen. Rebooting put it back.
Have you noticed the same diff between 7 and Vista?