Not sure if this is the same bug but I also get this too with 13.1,
Ubuntu 12.10 x86_64.

http://www.youtube.com/watch?v=4Fp8rpKaMT4

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https://bugs.launchpad.net/bugs/1067320

Title:
  1002:6798 [fglrx] VT cursor is visible and blinking on top of Unity
  Radeon HD 7970 and 5450

Status in “fglrx-installer” package in Ubuntu:
  Confirmed
Status in “unity” package in Ubuntu:
  Confirmed

Bug description:
  A black cursor is blinking on top of the screen.
  It is not as regular as a true shell prompt (because of glitches), but I'm 
sure this is the cursor of the underlying TTY.

  If I try to switch to any other TTY, the focus remains on the desktop
  (eg. I can still click and type in Firefox) but the black cursor does
  move as I type.

  For example, I just switched to TTY 1 and was able to log-in (I see it
  because of the cursor position on the screen), while my username and
  my password were also written in the text-box where I'm writing this
  bug report.

  This bug is really odd and annoying.

  ProblemType: Bug
  DistroRelease: Ubuntu 12.10
  Package: unity 6.8.0-0ubuntu2
  ProcVersionSignature: Ubuntu 3.5.0-17.28-generic 3.5.5
  Uname: Linux 3.5.0-17-generic x86_64
  NonfreeKernelModules: fglrx
  .tmp.unity.support.test.0:
   
  ApportVersion: 2.6.1-0ubuntu3
  Architecture: amd64
  CompizPlugins: No value set for 
`/apps/compiz-1/general/screen0/options/active_plugins'
  CompositorRunning: compiz
  Date: Tue Oct 16 13:34:59 2012
  DistUpgraded: Fresh install
  DistroCodename: quantal
  DistroVariant: ubuntu
  DkmsStatus:
   fglrx-updates, 9.000, 3.5.0-17-generic, x86_64: installed
   virtualbox, 4.1.18, 3.5.0-17-generic, x86_64: installed
  GraphicsCard:
   Advanced Micro Devices [AMD] nee ATI Tahiti XT [Radeon HD 7970] [1002:6798] 
(prog-if 00 [VGA controller])
     Subsystem: Micro-Star International Co., Ltd. Device [1462:2780]
  InstallationMedia: Ubuntu 12.10 "Quantal Quetzal" - Beta amd64 (20121004)
  MachineType: MSI MS-7752
  ProcEnviron:
   TERM=xterm
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=fr_FR.UTF-8
   SHELL=/bin/bash
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.5.0-17-generic 
root=UUID=9054a8bb-9c6c-4689-be51-a5fece8e4155 ro quiet splash vt.handoff=7
  SourcePackage: unity
  UpgradeStatus: No upgrade log present (probably fresh install)
  dmi.bios.date: 09/04/2012
  dmi.bios.vendor: American Megatrends Inc.
  dmi.bios.version: V2.6
  dmi.board.asset.tag: To be filled by O.E.M.
  dmi.board.name: Z77A-G45 (MS-7752)
  dmi.board.vendor: MSI
  dmi.board.version: 1.0
  dmi.chassis.asset.tag: To Be Filled By O.E.M.
  dmi.chassis.type: 3
  dmi.chassis.vendor: MSI
  dmi.chassis.version: 1.0
  dmi.modalias: 
dmi:bvnAmericanMegatrendsInc.:bvrV2.6:bd09/04/2012:svnMSI:pnMS-7752:pvr1.0:rvnMSI:rnZ77A-G45(MS-7752):rvr1.0:cvnMSI:ct3:cvr1.0:
  dmi.product.name: MS-7752
  dmi.product.version: 1.0
  dmi.sys.vendor: MSI
  version.compiz: compiz 1:0.9.8.4-0ubuntu2
  version.fglrx-installer: fglrx-installer N/A
  version.ia32-libs: ia32-libs N/A
  version.libdrm2: libdrm2 2.4.39-0ubuntu1
  version.libgl1-mesa-dri: libgl1-mesa-dri 9.0-0ubuntu1
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 9.0-0ubuntu1
  version.xserver-xorg-core: xserver-xorg-core 2:1.13.0-0ubuntu6
  version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.7.3-0ubuntu2
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 
1:6.99.99~git20120913.8637f772-0ubuntu1
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.20.9-0ubuntu2
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 
1:1.0.2-0ubuntu3

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