This also happens to me
On Virtualbox 4.1.12 Using latest Ubuntu 12.04 On Mac OS x 10.7.3 ATI X1900 
Graphic card

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https://bugs.launchpad.net/bugs/876999

Title:
  compiz doesn't show any windows with VirtualBox guest additions

Status in “compiz” package in Ubuntu:
  Confirmed
Status in “nautilus” package in Ubuntu:
  Confirmed

Bug description:
  Host configuration:
  VirtualBox 4.1.4 – Mac OS X 10.7.2

  Guest configuration:
  Ubuntu 11.10
  2 processors – 1 GB RAM
  128 MB video memory – 3D acceleration enabled

  The VirtualBox guest additions were installed through "Additional
  Drivers". After rebooting, all the UI is visible including the login
  screen and the Unity interface, but when any application is opened,
  its window is invisible.

  Notes:
  When the virtual machine is logged in with "Ubuntu 2D", I can run "compiz 
--replace" and get compiz working properly.
  The problem occurred on both a VM upgraded from 11.04 to 11.10 and a fresh 
install of 11.10 (used for screencasts below).
  The problem occurred using both the guest additions package from "Additional 
Drivers" and the guest additions ISO shipped with VirtualBox.

  "Ubuntu" video here: http://screencast.com/t/wZIug5RsG3fh
  "Ubuntu 2D" video here: http://screencast.com/t/R6LsrTVyIC

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