Below is a fix/workaround/solution that might work for some who are
visiting this thread.

Short version:
Stop using external video adapters and instead use the natively supported 
connections.

Medium version: 
Ubuntu 14.04 _AND_ 16.04. My problem started when I started using a external 
video adapter (hpk-481409-001 Displayport to DVI). It was solved by ceasing to 
use the video adapter and instead using the native connections of both the 
monitor and PC.

Long version:
I was running 14.04 on an HP Elitedesk 800 workstation with 2 Display ports and 
1 VGA port. I changed monitors and needed to start using an adapter for one of 
them since they only supported DVI input, the display ports on the PC were 
internally connected in parallel, and the Display port to DVI cables that I had 
only mapped the first channel. When the problem started, I thought that it was 
an Ubuntu update issue and it would resolve itself. I later upgraded from 14.04 
to 16.04 and the problem persisted. I tried switching to a heterogeneous 
monitor configuration like I had before the monitor change, because I thought 
that it might be a monitor-name identification issue, however this did not fix 
the problem. I tried using a VGA/Displayport combination (luckily for those 
reading this I, for some reason, kept the displayport-DVI-adapter connection), 
and that didn't solve the problem. Then, I simply replaced the 
displayport-DVI-adapter connection with a simple displayport-DVI cable, and I
  do not see the problem anymore. If it pops up again I will provide an update.

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https://bugs.launchpad.net/bugs/1295267

Title:
  Windows change Monitor/Desktop after screen lock

Status in Unity:
  Fix Released
Status in Unity 7.1 series:
  Fix Released
Status in compiz-plugins-main package in Ubuntu:
  Fix Released
Status in unity package in Ubuntu:
  Triaged

Bug description:
  I run a dual monitor configuration, with one portrait and one
  landscape.

  I nearly always have multiple applications open in multiple windows
  across both monitors and all virtual desktops.

  When I lock the screen and then unlock, my application windows will
  move from their original position.

  Sometimes they are in completely random positions;

  Other times they seem to get the monitors confused, and rather than
  being in the top half of the portrait monitor they are on the top half
  of the landscape monitor;

  Sometimes it is only a new desktop, but the monitor position is the
  same;

  Sometimes it is the same desktop, but on the other monitor.

  Description:  Ubuntu 13.10
  Release:      13.10

  What I expect to happen: When I unlock my computer, all the windows
  are in the same position on the same monitor and desktop as I left
  them.

  What actually happens: When I unlock my computer, some or all of the
  windows have been changed to a random position on a random monitor
  and/or desktop.

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