Public bug reported:

It seems to be duplicate of both :
https://bugs.launchpad.net/ubuntu/+source/xorg/+bug/1641467
and 
https://bugs.launchpad.net/ubuntu/+source/xorg/+bug/1629300  .
Possibly related to https://bugs.launchpad.net/ubuntu/+source/xorg/+bug/1278223

A - flickering in first display.
The zone starts just below the top panel and its height is about 1/7 of the 
screen.
Flickering starts immediately entering the zone, even half of the pointer may 
be flickering.
To the centre of the zone, flickering is more prevalent, up to completely 
disappearing. 
The flickering has a periodic pattern, which seems to be affected by the 
windows displaying in the second (external) monitor !! 

B - external monitor.
Some applications show really slow there. Worse case is HipChat (Atlassian chat 
program), which shows fine as long as even a tiny fraction exists on the 
primary display. 
At the moment the whole window passes to the secondary, then even the scroll 
bar has a delay of a second a move. 

To check, I have played with the ~/.config/monitors.xml without success.
It seems that each configuration is saved there, even duplicates, after adding 
the same external monitor and re-configuring it (absolute duplicate in 
monitors.xml)

C. Side-effects and related phenomena. 
Some times the "Screen display" control freaks, when enabling the external 
monitor. It may freeze or insist to put them in mirroring. Most of the times it 
just forgets a setup (although in monitors.xml) after adding a different 
external monitor.
For each workspace, there is a different background, done with Unit5y Tweak 
Tool. 

All updates have been done, without effect.

ProblemType: Bug
DistroRelease: Ubuntu 16.10
Package: xorg 1:7.7+13ubuntu4
ProcVersionSignature: Ubuntu 4.8.0-27.29-generic 4.8.1
Uname: Linux 4.8.0-27-generic x86_64
.tmp.unity_support_test.0:
 
ApportVersion: 2.20.3-0ubuntu8
Architecture: amd64
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: Tue Nov 29 23:18:52 2016
DistUpgraded: Fresh install
DistroCodename: yakkety
DistroVariant: ubuntu
DkmsStatus: virtualbox, 5.1.6, 4.8.0-27-generic, x86_64: installed
ExtraDebuggingInterest: Yes
GraphicsCard:
 Intel Corporation HD Graphics 530 [8086:191b] (rev 06) (prog-if 00 [VGA 
controller])
   Subsystem: Lenovo HD Graphics 530 [17aa:222e]
 NVIDIA Corporation GM107GLM [Quadro M1000M] [10de:13b1] (rev a2) (prog-if 00 
[VGA controller])
   Subsystem: Lenovo GM107GLM [Quadro M1000M] [17aa:222e]
InstallationDate: Installed on 2016-11-09 (20 days ago)
InstallationMedia: Ubuntu 16.10 "Yakkety Yak" - Release amd64 (20161012.2)
MachineType: LENOVO 20EN0019US
ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.8.0-27-generic.efi.signed 
root=UUID=c3151b80-1188-4c23-816c-57ebe18688a8 ro quiet splash vt.handoff=7
SourcePackage: xorg
UpgradeStatus: No upgrade log present (probably fresh install)
dmi.bios.date: 08/03/2016
dmi.bios.vendor: LENOVO
dmi.bios.version: N1EET57W (1.30 )
dmi.board.asset.tag: Not Available
dmi.board.name: 20EN0019US
dmi.board.vendor: LENOVO
dmi.board.version: SDK0J40705 WIN
dmi.chassis.asset.tag: No Asset Information
dmi.chassis.type: 10
dmi.chassis.vendor: LENOVO
dmi.chassis.version: None
dmi.modalias: 
dmi:bvnLENOVO:bvrN1EET57W(1.30):bd08/03/2016:svnLENOVO:pn20EN0019US:pvrThinkPadP50:rvnLENOVO:rn20EN0019US:rvrSDK0J40705WIN:cvnLENOVO:ct10:cvrNone:
dmi.product.name: 20EN0019US
dmi.product.version: ThinkPad P50
dmi.sys.vendor: LENOVO
version.compiz: compiz 1:0.9.13.0+16.10.20160818.2-0ubuntu2
version.ia32-libs: ia32-libs N/A
version.libdrm2: libdrm2 2.4.70-1
version.libgl1-mesa-dri: libgl1-mesa-dri 12.0.3-1ubuntu2
version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
version.libgl1-mesa-glx: libgl1-mesa-glx 12.0.3-1ubuntu2
version.xserver-xorg-core: xserver-xorg-core 2:1.18.4-1ubuntu6.1
version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.10.2-1ubuntu1
version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:7.7.1-1
version.xserver-xorg-video-intel: xserver-xorg-video-intel 
2:2.99.917+git20160706-1ubuntu1
version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 1:1.0.12-2
xserver.bootTime: Fri Nov 25 08:07:33 2016
xserver.configfile: default
xserver.logfile: /var/log/Xorg.0.log
xserver.version: 2:1.18.4-1ubuntu6.1
xserver.video_driver: modeset

** Affects: xorg (Ubuntu)
     Importance: Undecided
         Status: New


** Tags: amd64 apport-bug compiz-0.9 ubuntu yakkety

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https://bugs.launchpad.net/bugs/1645891

Title:
  After adding a second monitor, mouse pointer flickers and/or
  disappears in a zone near the top of first (notebook) monitor, while
  some apps show slow in ext display.

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