So just FYI, this is actually 3 bugs in one:

The first was only really happening internally, and that was when we
were not tracking menus since they were override-redirect sometimes.
That is now fixed, and will be pushed along with the fix for crashing
flash in chromium and the crashing gnome-panel applets on load.

The second appears to be some kind of race condition where we are not
getting damage events - Either this was caused by some change in the X
Server (unlikely, since it doesn't happen with compiz 0.8) or we are
using the damage extension wrong (also seems unlikely, since the damage
extension is relatively simple, but we could still be using it
incorrectly). I'm currently looking into this with the Xorg people and
doing some debugging in XComposite itself to see what is going on. (You
can reproduce this one if you click to trigger menu creation and nothing
appears in some cases, but if you hover over where the menu should be,
it will then appear).

The third is a stacking issue and this has been around for ages and will
be looked into after the XComposite issue.

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https://bugs.launchpad.net/bugs/693073

Title:
  Panel and application Menus working but not visible

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