I'm also getting this bug on Precise. This is very reproducible with
applications set to start on login, like alarm-clock-applet. The top
panel obscures the titlebar for the window, making an Alt+drag necessary
to drag the window out; the window is impossible to close if you don't
know keyboard shortcuts for window management.

Also, if the launcher is set to its default of being always visible, the
window(s) will appear underneath that, as well, which just looks weird.

** Tags added: precise

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https://bugs.launchpad.net/bugs/861879

Title:
  restarting unity causes that window top bar is under top panel

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