I have the same problem on a fresh install of 12.04.1-amd64 with all
updates.

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https://bugs.launchpad.net/bugs/928930

Title:
  Scrolling using the center wheel bounces

Status in “xserver-xorg-input-evdev” package in Ubuntu:
  Fix Released

Bug description:
  When using the middle scroll wheel of the mouse, if scrolling down,
  the webpage or document bounces back up, and vice-versa. This issue is
  found in gedit, firefox, anything requireing scrolling. I don't have
  the same issue on either Ubuntu 10.04 nor Windows on the same machine.
  This problem has been around now for roughly a week, and no updates
  have corrected the issue.

  Release information:
  Description:  Ubuntu precise (development branch)
  Release:      12.04

  xorg:
    Installed: 1:7.6+10ubuntu1
    Candidate: 1:7.6+10ubuntu1
    Version table:
   *** 1:7.6+10ubuntu1 0
          500 http://us.archive.ubuntu.com/ubuntu/ precise/main amd64 Packages
          100 /var/lib/dpkg/status

  Expected:
       Smooth movement up and down using the scroll wheel

  Actual: 
       Bouncing of the page up and down in opposition to the direction of 
scrolling.

  All packages are up to date as per the time of filing this bug report
  :).

  ProblemType: Bug
  DistroRelease: Ubuntu 12.04
  Package: xorg 1:7.6+10ubuntu1
  ProcVersionSignature: Ubuntu 3.2.0-14.23-generic 3.2.3
  Uname: Linux 3.2.0-14-generic x86_64
  .tmp.unity.support.test.0:
   
  ApportVersion: 1.91-0ubuntu1
  Architecture: amd64
  CompizPlugins: 
[core,bailer,detection,composite,opengl,decor,place,session,imgpng,move,compiztoolbox,vpswitch,mousepoll,resize,wall,snap,grid,gnomecompat,regex,animation,fade,expo,workarounds,ezoom,scale,unityshell]
  CompositorRunning: compiz
  Date: Wed Feb  8 07:37:42 2012
  DistUpgraded: Log time: 2012-02-01 07:23:38.688871
  DistroCodename: precise
  DistroVariant: ubuntu
  ExtraDebuggingInterest: Yes, if not too technical
  GraphicsCard: InnoTek Systemberatung GmbH VirtualBox Graphics Adapter 
[80ee:beef] (prog-if 00 [VGA controller])
  InstallationMedia: Ubuntu 11.10 "Oneiric Ocelot" - Release amd64 (20111012)
  Lsusb:
   Bus 001 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
   Bus 001 Device 002: ID 80ee:0021 VirtualBox USB Tablet
  MachineType: innotek GmbH VirtualBox
  ProcEnviron:
   PATH=(custom, no user)
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-3.2.0-14-generic 
root=UUID=64cc9267-db3f-4f41-9e0b-505ba8ecd01c ro quiet splash vt.handoff=7
  Renderer: Software
  SourcePackage: xorg
  UpgradeStatus: Upgraded to precise on 2012-02-01 (6 days ago)
  dmi.bios.date: 12/01/2006
  dmi.bios.vendor: innotek GmbH
  dmi.bios.version: VirtualBox
  dmi.modalias: 
dmi:bvninnotekGmbH:bvrVirtualBox:bd12/01/2006:svninnotekGmbH:pnVirtualBox:pvr1.2:
  dmi.product.name: VirtualBox
  dmi.product.version: 1.2
  dmi.sys.vendor: innotek GmbH
  version.compiz: compiz 1:0.9.6+bzr20110929-0ubuntu8
  version.ia32-libs: ia32-libs N/A
  version.libdrm2: libdrm2 2.4.30-1ubuntu1
  version.libgl1-mesa-dri: libgl1-mesa-dri 8.0~rc2-0ubuntu4
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 8.0~rc2-0ubuntu4
  version.xserver-xorg-core: xserver-xorg-core 2:1.11.3-0ubuntu10
  version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 
1:2.6.99.901-1ubuntu3
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 
1:6.14.99~git20111219.aacbd629-0ubuntu2
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 2:2.17.0-1ubuntu3
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 
1:0.0.16+git20111201+b5534a1-1build2

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