Comment 73 for bug 805087

Okay, the trigger here is disabling Nautilus managing the desktop. If you head to gnome-tweak-tool and turn on “Have file manager handle the desktop,” the problem should go away. (In place of a new problem, of course, but we're getting somewhere).

This does seem to line up with the behaviour I noted above, with Nautilus being that one open window that keeps the dash from breaking. As well as the setting in gnome-tweak-tool, Nautilus crashing (or being force killed) triggers this. And I'd bet there's a race condition at login, too.

This might prove enlightening:
With Nautilus handling the desktop, if I close all open windows, then force kill Nautilus, then open another application that is not Nautilus, the dash will appear beneath that window. (As before).
If I then open Nautilus (which automatically starts handling the desktop again) the dash will begin to appear on top of open windows.

You can reproduce this absolutely reliably, on any computer, by opening gnome-tweak-tool, turning off “file manager handles the desktop,” and logging in again.

Hopefully that makes it a little clearer what's going on here :)

Would you like me to open a new bug report, or are these indeed the same problems?