It would be easier to reproduce on a bare X.

If you do from a vt:

sudo service ligthdm stop
sudo Xorg -ac -noreset & sleep 3; DISPLAY=:0 xterm

then launch glxgears from the xterm, does it show the behaviour we need to fix?
i.e. runs at below refresh rate unless there is another source of interrupts 
(e.g. wiggling the mouse)?

If you can reproduce that, we can begin to test the patches.

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https://bugs.launchpad.net/bugs/1087582

Title:
  [gen3] Bad GPU performance whilst CPU is in deep sleep

Status in X.org xf86-video-intel:
  Incomplete
Status in “xserver-xorg-video-intel” package in Ubuntu:
  Incomplete

Bug description:
  I have an Acer AOD250(KAV60) netbook.
  On Ubuntu 12.10 with glxgears I get 50-60 fps, while on Lubuntu I get half 
that and sometimes worse.
  The odd thing about this is that when I start moving my mouse around it 
straightens up and goes back to roughly 55-60 fps, and once I stop moving the 
mouse, the performance drops again.
  I know the chipset and GPU isn't the best out there, but it shouldn't be 
acting like this(before, I was able to use Celestia with ease but now I get 
below 5 fps).

  Latest available BIOS(v1.29)
  Intel Atom N270 1.6GHz(1 core, 2 threads)
  1024RAM
  Intel 945GMA(8MB VRAM from BIOS)

  Tested glxgears from mesa-utils "8.0.1+git20110129+d8f7d6b-0ubuntu2"

  ProblemType: Bug
  DistroRelease: Ubuntu 12.10
  Package: xserver-xorg-video-intel 2:2.20.9-0ubuntu2
  ProcVersionSignature: Ubuntu 3.5.0-19.30-generic 3.5.7
  Uname: Linux 3.5.0-19-generic i686
  ApportVersion: 2.6.1-0ubuntu6
  Architecture: i386
  Date: Fri Dec  7 02:37:04 2012
  InstallationDate: Installed on 2012-12-07 (0 days ago)
  InstallationMedia: Lubuntu 12.10 "Quantal Quetzal" - Release i386 (20121017.1)
  MarkForUpload: True
  SourcePackage: xserver-xorg-video-intel
  UpgradeStatus: No upgrade log present (probably fresh install)

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