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a60fb26
(Get the code!)
For me, it happens immediately after login with a firefox window. I don't need any steps to reproduce it (this is obviously unworkable, so I'm using gnome-shell at the moment).
I've tried to experiment with this a bit more.
* This happens every time at logon. The first window is always above the dash if it is maximized, and sometimes if it is not. It seems that either all or no windows are on top of the dash.
* I cannot seem to find any reproducible steps to stop this behaviour, even though it occasionally disappears and comes back during a session.
* The problem disappears after running unity --replace in a terminal window.
I've attached my .xsession-errors of a session showing this behaviour.
I can get you some info about X / compiz internal state if you tell me what debug packages to install, where to set a breakpoint and what to look for.