I have observed the same issue after upgrading from Xubuntu 15.10 to
Xubuntu 16.04. Just as fabiomarconi described the cursor reappeared
after clicking the logout-button. I use real hardware, no
virtualization.

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https://bugs.launchpad.net/bugs/1540157

Title:
  Xenial: Mouse pointer disappears after release upgrade

Status in unity package in Ubuntu:
  Confirmed
Status in xserver-xorg-video-intel package in Ubuntu:
  Incomplete

Bug description:
  After release upgrade from Wily to Xenial, the mouse pointer is
  invisible.

  Reproduce:
  – Install Ubuntu Wily Werewolf desktop from the official Live CD.
  – Upgrade to Xenial Xerus with „do-release-upgrade -d”.

  Only had a chance to test it on KVM virtual machine, but it happened every 
time I upgraded a virtual machine to Xenial.
  Also, only tested via Wily -> Xenial upgrade, haven't tried Trusty -> Xenial.

  Nature Xenial install from the Xenial Live CD daily build right away
  doesn't have this issue, so I assume something goes wrong during the
  upgrade process.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: unity 7.4.0+16.04.20151218-0ubuntu2
  ProcVersionSignature: Ubuntu 4.3.0-7.18-generic 4.3.3
  Uname: Linux 4.3.0-7-generic x86_64
  .tmp.unity.support.test.1:
   
  ApportVersion: 2.19.4-0ubuntu1
  Architecture: amd64
  BootLog:
   
  CompizPlugins: No value set for 
`/apps/compiz-1/general/screen0/options/active_plugins'
  CompositorRunning: compiz
  CompositorUnredirectDriverBlacklist: '(nouveau|Intel).*Mesa 8.0'
  CompositorUnredirectFSW: true
  CurrentDesktop: Unity
  Date: Sun Jan 31 22:45:19 2016
  DistUpgraded: 2016-01-31 21:18:14,758 DEBUG enabling apt cron job
  DistroCodename: xenial
  DistroVariant: ubuntu
  GraphicsCard:
   Red Hat, Inc. QXL paravirtual graphic card [1b36:0100] (rev 04) (prog-if 00 
[VGA controller])
     Subsystem: Red Hat, Inc QEMU Virtual Machine [1af4:1100]
  InstallationDate: Installed on 2016-01-31 (0 days ago)
  InstallationMedia: Ubuntu 15.10 "Wily Werewolf" - Release amd64 (20151021)
  Lsusb:
   Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
   Bus 004 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
   Bus 003 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
   Bus 002 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
  MachineType: QEMU Standard PC (i440FX + PIIX, 1996)
  ProcKernelCmdLine: BOOT_IMAGE=/vmlinuz-4.3.0-7-generic 
root=/dev/mapper/wvg-root ro
  Renderer: Software
  SourcePackage: unity
  UpgradeStatus: Upgraded to xenial on 2016-01-31 (0 days ago)
  dmi.bios.date: 04/01/2014
  dmi.bios.vendor: SeaBIOS
  dmi.bios.version: Ubuntu-1.8.2-1ubuntu1
  dmi.chassis.type: 1
  dmi.chassis.vendor: QEMU
  dmi.chassis.version: pc-i440fx-vivid
  dmi.modalias: 
dmi:bvnSeaBIOS:bvrUbuntu-1.8.2-1ubuntu1:bd04/01/2014:svnQEMU:pnStandardPC(i440FX+PIIX,1996):pvrpc-i440fx-vivid:cvnQEMU:ct1:cvrpc-i440fx-vivid:
  dmi.product.name: Standard PC (i440FX + PIIX, 1996)
  dmi.product.version: pc-i440fx-vivid
  dmi.sys.vendor: QEMU
  version.compiz: compiz 1:0.9.12.2+16.04.20151211-0ubuntu1
  version.ia32-libs: ia32-libs N/A
  version.libdrm2: libdrm2 2.4.66-2
  version.libgl1-mesa-dri: libgl1-mesa-dri 11.1.1-1ubuntu2
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 11.1.1-1ubuntu2
  version.xserver-xorg-core: xserver-xorg-core 2:1.17.3-2ubuntu2
  version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.9.2-1ubuntu1
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:7.6.1-1
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 
2:2.99.917+git20151217-1~exp1ubuntu1
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 1:1.0.12-1
  xserver.bootTime: Sun Jan 31 22:44:03 2016
  xserver.configfile: default
  xserver.devices:
   input        Power Button         KEYBOARD, id 6
   input        AT Translated Set 2 keyboard KEYBOARD, id 7
   input        VirtualPS/2 VMware VMMouse MOUSE, id 8
   input        VirtualPS/2 VMware VMMouse TOUCHSCREEN, id 9
   input        spice vdagent tablet TOUCHSCREEN, id 10
  xserver.errors:
   systemd-logind: failed to get session: PID 700 does not belong to any known 
session
   AIGLX: reverting to software rendering
   qxl(0): EXECBUFFER failed
  xserver.logfile: /var/log/Xorg.0.log
  xserver.outputs: Output                               Virtual-0       
Virtual-1       Virtual-2       Virtual-3
  xserver.version: 2:1.17.3-2ubuntu2
  xserver.video_driver: qxl

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