Comment 4 for bug 573986

The problem also exists on Ubuntu 12.04 64 Bit.

If you minimise the virtualbox-window, the notify-popups start to work, even when the virtual machine is running and not paused. But after restoring the minimised window, the problem occurs again: If there is currently a notify-popup visible while you restore the VM-window, it behaves normal (it is displayed in the foreground of the VM-window and fades out after its lifetime) but no new notifies are displayed.

You can test this behaviour with the notify-send command of the libnotify-bin package.