I am still seeing this in 12.10. I have only seen this happen with
virtualbox in seamless mode, and it does affect all indicators. The
indicator menu will not display even on a separate monitor from the one
where seamless mode is active, yet it does reliably draw the decoration
on the panel as if the menu was displayed (see attachment).

Once VirtualBox has focus the indicator menus can be displayed in two
ways: 1) giving focus to another non-seamless window, or 2) hitting the
VirtualBox hostkey, which defaults to Right Ctrl for me, and reselecting
a different indicator.

** Attachment added: "the indicator background on the panel is drawn as if the 
menu is displayed even though the menu that extends below the panel is not"
   
https://bugs.launchpad.net/ubuntu/+source/gnome-panel/+bug/706416/+attachment/3451775/+files/virtualbox_seamless_indicator_menus.png

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https://bugs.launchpad.net/bugs/706416

Title:
  Indicator menus won't open when a VirtualBox seamless VM has focus

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