I had an old hard drive around, so I installed Ubuntu to it.

I installed the latest kernel from that link (v4.8-rc5), and the bug is fixed 
there.
I haven't installed the NVidia proprietary drivers.

$ uname -a
Linux bruno-mitsai 4.8.0-040800rc5-generic #201609041832 SMP Sun Sep 4 22:34:01 
UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 16.04.1 LTS
Release:        16.04
Codename:       xenial

** Tags added: kernel-fixed-upstream kernel-fixed-upstream-4.8-rc5

** Changed in: xorg-server (Ubuntu)
       Status: Incomplete => Confirmed

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https://bugs.launchpad.net/bugs/1585329

Title:
  Sometimes a black rectangle appears briefly under the mouse cursor

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