I had this problem repeatedly on Oneiric; couldn't see the trigger which
caused it. However I appear to have found a solution following the
suggestion above from Dylan McCall.

First, though a feature of my problem I didn't see noted above: when the
launcher slides underneath the windows in the viewport, if they're not
maximised, then clicking on the topmost overlying window, still launches
the application from the launcher as if the launcher were the topmost
window. Visually displayed at the back of the stack, but still at the
front from the point of view of viewport events. (If an overlying window
is maximised, then clicking on over the area where the launcher should
be doesn't produce this effect.)

I noticed Dylan's comments about nautilus. I checked gnome-tweak and
found I had "have file manager handle the desktop" turned off. However,
rather than turn it on, I fired up gconf-editor and I found that "show
desktop" and "show desktop as home" in the nautilus preferences were
still enabled (the things you used to tweak to get nautilus to draw the
desktop, and enable right-click on desktop). I disabled both - useless
now as they don't bring the right-click on the desktop back - and since
then I haven't seen the problem. With this, even killall nautilus
doesn't precipitate the problem anymore and the launcher is well
behaved.

Perhaps it's possible to arrive at incompatible gconf options at this
point in the transition to Unity? I guess this shouldn't produce the
effects above still, but I'm just happy to have a solution. Thanks
Dylan! Anyone else experienced similar?

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https://bugs.launchpad.net/bugs/805087

Title:
  Dash and launcher appear underneath windows

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