I'm not a Ubuntu user myself, but seeing the exact same issue on my
Gentoo (unstable) system. I've seen it before the last couple of months,
but only occasionally, typically after a long-running X session and it
usually went away with an X server restart. For a bit over a week now
the problem has been permanent however.

X.Org 1.15.0, xf86-video-intel 2.99.910, Mesa 10.1.0 (also seen with
9.2.5), Linux 3.13.3, Gnome 3 Shell

OpenGL renderer string: Mesa DRI Intel(R) Sandybridge Mobile 
[ 27305.329] (--) intel(0): Integrated Graphics Chipset: Intel(R) HD Graphics 
3000

Notice that there is a 256x256 area in the lower left corner of the
window in which the window is not translucent. This corner always stays
there independent of window resizes or going fullscreen. For the rest of
the window it looks like its content are being "added" to the
background.

I've seen this bug posted in various places, like reported as a
Minecraft bug or as LWJGL bug (the Java-GL glue library). It's certainly
not a Minecraft bug, as it apparently appears with LWJGL demo
applications as well. All the bug reports seem to have Intel onboard
graphics in common.

Note that there are also reports for a similar bug on Windows, but I
doubt it's related.

-- 
You received this bug notification because you are a member of Desktop
Packages, which is subscribed to xserver-xorg-video-intel in Ubuntu.
https://bugs.launchpad.net/bugs/1277905

Title:
  Game windows (minecraft, titan attacks, maybe others) on Intel are
  transparent and no longer playable

Status in “xserver-xorg-video-intel” package in Ubuntu:
  Confirmed

Bug description:
  Fully up to date Trusty.
  Open Minecraft, notice that the window is transparent - you can see through 
to the desktop wallpaper, making the game unplayable.
  Also tested with Titan Attacks which is also a lwjgl based game - dunno if 
that's coincidence

  This worked a few days ago. Probably before the most recent xorg
  update.

  See screenshots.

  ProblemType: Bug
  DistroRelease: Ubuntu 14.04
  Package: xserver-xorg-video-intel 2:2.99.909-0ubuntu2
  ProcVersionSignature: Ubuntu 3.13.0-7.25-generic 3.13.1
  Uname: Linux 3.13.0-7-generic x86_64
  .tmp.unity.support.test.0:
   
  ApportVersion: 2.13.2-0ubuntu2
  Architecture: amd64
  CompizPlugins: 
[core,composite,opengl,compiztoolbox,decor,grid,imgpng,gnomecompat,scale,workarounds,mousepoll,regex,wall,move,place,vpswitch,resize,unitymtgrabhandles,snap,session,expo,ezoom,unityshell]
  CompositorRunning: compiz
  CompositorUnredirectDriverBlacklist: '(nouveau|Intel).*Mesa 8.0'
  CompositorUnredirectFSW: true
  CurrentDesktop: Unity
  Date: Sat Feb  8 10:54:09 2014
  DistUpgraded: 2014-01-20 08:54:25,315 DEBUG enabling apt cron job
  DistroCodename: trusty
  DistroVariant: ubuntu
  EcryptfsInUse: Yes
  ExtraDebuggingInterest: Yes
  GraphicsCard:
   Intel Corporation 2nd Generation Core Processor Family Integrated Graphics 
Controller [8086:0126] (rev 09) (prog-if 00 [VGA controller])
     Subsystem: Lenovo Device [17aa:21da]
  InstallationDate: Installed on 2012-06-29 (588 days ago)
  InstallationMedia: Ubuntu 12.04 LTS "Precise Pangolin" - Release amd64 
(20120425)
  MachineType: LENOVO 4287CTO
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.13.0-7-generic 
root=UUID=6088859e-4fc3-4ec8-903f-5b52cdc1d0eb ro quiet splash vt.handoff=7
  SourcePackage: xserver-xorg-video-intel
  UpgradeStatus: Upgraded to trusty on 2014-01-20 (19 days ago)
  dmi.bios.date: 12/05/2012
  dmi.bios.vendor: LENOVO
  dmi.bios.version: 8DET67WW (1.37 )
  dmi.board.asset.tag: Not Available
  dmi.board.name: 4287CTO
  dmi.board.vendor: LENOVO
  dmi.board.version: Not Available
  dmi.chassis.asset.tag: No Asset Information
  dmi.chassis.type: 10
  dmi.chassis.vendor: LENOVO
  dmi.chassis.version: Not Available
  dmi.modalias: 
dmi:bvnLENOVO:bvr8DET67WW(1.37):bd12/05/2012:svnLENOVO:pn4287CTO:pvrThinkPadX220:rvnLENOVO:rn4287CTO:rvrNotAvailable:cvnLENOVO:ct10:cvrNotAvailable:
  dmi.product.name: 4287CTO
  dmi.product.version: ThinkPad X220
  dmi.sys.vendor: LENOVO
  version.compiz: compiz 1:0.9.10+13.10.20131011-0ubuntu4
  version.ia32-libs: ia32-libs N/A
  version.libdrm2: libdrm2 2.4.52-1
  version.libgl1-mesa-dri: libgl1-mesa-dri 10.0.1-1ubuntu2
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 10.0.1-1ubuntu2
  version.xserver-xorg-core: xserver-xorg-core 2:1.15.0-1ubuntu3
  version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.8.2-1ubuntu2
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:7.3.0-1ubuntu2
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.99.909-0ubuntu2
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 
1:1.0.10-1ubuntu2
  xserver.bootTime: Sat Feb  8 10:50:45 2014
  xserver.configfile: default
  xserver.errors:
   
  xserver.logfile: /var/log/Xorg.0.log
  xserver.outputs:
   product id                                 728 
   vendor                                     LGD
  xserver.version: 2:1.15.0-1ubuntu3

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