Comment 72 for bug 805087

For me, too, this happens immediately, absolutely every time I log in to a Unity 3D session in Ubuntu 11.10. Really, it's like this: “Log in to Unity. Open any application from the launcher. (Try to) open the dash.” With that process, the dash in the third step reliably appears beneath any toplevel window.

Here are a few details of my setup. I hope they can help a little to find the source of the remaining problems:
 * I have an ATI Radeon 6870 GPU. I am using the free driver that comes by default in Ubuntu, not fglrx.
 * Since I usually run Gnome Shell, I also usually have the Adwaita theme enabled. I haven't noticed this affecting things, but who knows?
 * I have removed appmenu-*, so the global menu feature is disabled in Unity on my system.
 * I have turned off Nautilus managing my desktop.

If I have any open windows and then run unity --reset in the terminal, when Unity comes back up the dash _will_ properly appear over open windows. If I run unity --reset with all windows either minimized or closed (nothing open) then Unity will behave as when I log in fresh: the dash will appear beneath open windows.

In the first case, with the dash behaving properly, if I proceed to _close_ every open window, then open another window, Unity's dash will appear beneath that window again.