I can confirm the relation to Java based apps. I'm back on Ubuntu
(default) session and i still experience this problem when Netbeans 8
(Java based) is opened. After i close Netbeans, Skype windows are not
corrupted anymore.

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Touch seeded packages, which is subscribed to xorg in Ubuntu.
https://bugs.launchpad.net/bugs/1507484

Title:
  Window Graphics Corrupted for Skype

Status in xorg package in Ubuntu:
  Incomplete

Bug description:
  After update to pre-release ubuntu 15.10, skype window graphics is
  corrupted. Resizing and moving the window do not help. Till now, skype
  is the only application having this.

  ProblemType: Bug
  DistroRelease: Ubuntu 15.10
  Package: xorg 1:7.7+7ubuntu4
  ProcVersionSignature: Ubuntu 4.2.0-16.19-generic 4.2.3
  Uname: Linux 4.2.0-16-generic x86_64
  .tmp.unity.support.test.0:
   
  ApportVersion: 2.19.1-0ubuntu2
  Architecture: amd64
  BootLog:
   fsck from util-linux 2.26.2
   /dev/sda5: clean, 654139/11739136 files, 12149761/46937856 blocks
  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: Mon Oct 19 09:52:18 2015
  DistUpgraded: 2015-10-18 22:05:24,442 DEBUG enabling apt cron job
  DistroCodename: wily
  DistroVariant: ubuntu
  DkmsStatus:
   virtualbox, 5.0.4, 3.19.0-30-generic, x86_64: installed
   virtualbox, 5.0.4, 4.2.0-16-generic, x86_64: installed
  EcryptfsInUse: Yes
  ExtraDebuggingInterest: Yes, if not too technical
  GraphicsCard:
   Intel Corporation Haswell-ULT Integrated Graphics Controller [8086:0a16] 
(rev 0b) (prog-if 00 [VGA controller])
     Subsystem: Dell Device [1028:05ca]
  InstallationDate: Installed on 2014-11-03 (349 days ago)
  InstallationMedia: Ubuntu 14.04.1 LTS "Trusty Tahr" - Release amd64 
(20140722.2)
  MachineType: Dell Inc. Latitude E7240
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.2.0-16-generic 
root=UUID=4b8a3a17-f006-45f8-b65f-397b75c1d209 ro quiet splash vt.handoff=7
  SourcePackage: xorg
  Symptom: display
  UpgradeStatus: Upgraded to wily on 2015-10-18 (0 days ago)
  dmi.bios.date: 05/01/2014
  dmi.bios.vendor: Dell Inc.
  dmi.bios.version: A09
  dmi.board.name: 05PTPV
  dmi.board.vendor: Dell Inc.
  dmi.board.version: A00
  dmi.chassis.type: 9
  dmi.chassis.vendor: Dell Inc.
  dmi.modalias: 
dmi:bvnDellInc.:bvrA09:bd05/01/2014:svnDellInc.:pnLatitudeE7240:pvr01:rvnDellInc.:rn05PTPV:rvrA00:cvnDellInc.:ct9:cvr:
  dmi.product.name: Latitude E7240
  dmi.product.version: 01
  dmi.sys.vendor: Dell Inc.
  version.compiz: compiz 1:0.9.12.2+15.10.20151015-0ubuntu1
  version.ia32-libs: ia32-libs N/A
  version.libdrm2: libdrm2 2.4.64-1
  version.libgl1-mesa-dri: libgl1-mesa-dri 11.0.2-1ubuntu4
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 11.0.2-1ubuntu4
  version.xserver-xorg-core: xserver-xorg-core 2:1.17.2-1ubuntu9
  version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.9.2-1ubuntu1
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 
1:7.5.0+git20150819-0ubuntu1
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 
2:2.99.917+git20150808-0ubuntu4
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 
1:1.0.11-1ubuntu3
  xserver.bootTime: Sun Oct 18 22:05:47 2015
  xserver.configfile: default
  xserver.errors: intel(0): sna_mode_check: invalid state found on pipe 1, 
disabling CRTC:25
  xserver.logfile: /var/log/Xorg.0.log
  xserver.outputs:
   product id                                8300 
   vendor                                     AUO
  xserver.version: 2:1.17.2-1ubuntu9

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