Here's what it boils down to.
I've fought with this for years, and 9 times out of 10, I've found *something*
has tried to notify me of something. It may be a 3rd party app trying to bring its
window to the foreground, or an icon in the tray area, either visible or hidden,
trying to show me a message, or Windows Explorer itself trying to show me
a new window (such as from a recently inserted USB drive). Back in the days of win 95/98, if an
app wanted to bring a window to the foreground it simply did it. Boom, there it was. With
(XP?), Vista and Win7 though, instead of bringing the window or message to the foreground,
it just flashes the window's icon in the task bar or tray and a side effect is to unhide
the task bar if it's hidden, until the window or message is acknowledged with a click.
It's a feature to prevent popup windows from getting in your way and there are
good security reasons to not allow rouge popups to take immediate focus.
The *bug* in Windows 7, is that the flashing or highlighting of the icon in taskbar or tray
area just stops flashing and now there's no way to know what it was that was
trying to get your attention. The taskbar won't auto-hide until you acknowledge
the window, but there's no indication of which window it was. A hidden
tray icon may be trying to tell you something, but there's no indication now
which one it was. I know this to be the case, because if I go through and literally
click on and bring focus to *every single* window in the task bar, and every single icon in
the tray area, 9 times out of 10, I'll eventually stumble on the one that was trying to
tell me something, and as soon as I give it focus, the task bar hides again.
If I've got a lot of open windows, it may not be worth the hassle, and I'll just kill
and restart Windows Explorer.
I wish there was some way to kick windows explorer in the shin so it indicates what
window/alert is trying to get my attention *again*. Or a 3rd party app to clear that alert.