I have this problem in Ubuntu 14.04 and 16.04 with a dual 4K screen
setup (using a nvidia GPU).

Sometimes when waking the screens from standby ("Power Save Mode"), windows on 
the right screen are moved to an invisible offscreen area.
Using keyboard shortcuts, they can be moved to the visible area again.

I just ran my screens through ~10 standby cycles in different configurations.
One screen (Dell) wakes from standby almost immediately - the other (Iiyama) 
needs around 3 seconds. For simplicity, I will refer to them as quick and slow 
screen.
Both screens are connected via DisplayPort.
The driver from Ubuntu's nvidia-361 package is used.

I made the following observations:
* Window displacement happens on the right screen only.
* When the quick screen is the right screen, you can see the windows at the 
correct positions after wakeup, then the slow screen wakes up, reinitialization 
seems to be triggered (both screens are black for one second) and after that 
the windows are displaced (sometimes).
* When the quick screen is the right screen, random displacement seems to 
happen only once per Unity Session (if I logged out and in again, it happened 
again). When the slow screen is the right screen, it happens more often.
* When window displacement occurs, windows seem to be swapped between the right 
screen and the invisible offscreen area (-> windows still in the invisible 
offscreen area reappear at their former positions).
* Swapping the DisplayPort connectors at the Graphics Adapter does not have an 
impact on the behaviour.
* KDE also displaces windows on wakeup. They are moved to screen edges instead 
of invisible offscreen areas.

---

I am using the tint2 taskbar (window displacement also occurs without tint2). 
Its command line output at screen wakeup might be interesting.
There are two variants of output (see below). Window displacement may occur on 
either.
If displacement occurs, tint2 and also the menus in the title bar are often 
broken on one screen - until I restart tint2.

First variant:

/build/tint2-6JO0z5/tint2-0.12.7/src/tint.c 1163: triggering tint2 restart due 
to configuration change in the root window
/build/tint2-6JO0z5/tint2-0.12.7/src/tint.c 1883: restarting tint2...
xRandr: Found crtc's: 3
xRandr: Linking output DP-2 with crtc 0
xRandr: Linking output DP-4 with crtc 1
xsettings: Gtk/FontName = Ubuntu 11
xsettings: Net/IconThemeName = ubuntu-mono-dark
real transparency on... depth: 32
panel items: TSC
Systray composited rendering on
tint2 : nb monitor 2, nb monitor used 2, nb desktop 1
Kernel uevent interface initialized...

Second variant:

/build/tint2-6JO0z5/tint2-0.12.7/src/tint.c 1163: triggering tint2 restart due 
to configuration change in the root window
/build/tint2-6JO0z5/tint2-0.12.7/src/tint.c 1883: restarting tint2...
xRandr: Found crtc's: 3
xRandr: Linking output DP-2 with crtc 0
xsettings: Gtk/FontName = Ubuntu 11
xsettings: Net/IconThemeName = ubuntu-mono-dark
real transparency on... depth: 32
panel items: TSC
Systray composited rendering on
tint2 : nb monitor 1, nb monitor used 1, nb desktop 2
Kernel uevent interface initialized...
tint2 : another systray is running pid=1908
/build/tint2-6JO0z5/tint2-0.12.7/src/tint.c 1163: triggering tint2 restart due 
to configuration change in the root window
/build/tint2-6JO0z5/tint2-0.12.7/src/tint.c 1883: restarting tint2...
xRandr: Found crtc's: 3
xRandr: Linking output DP-2 with crtc 0
xRandr: Linking output DP-4 with crtc 1
xsettings: Gtk/FontName = Ubuntu 11
xsettings: Net/IconThemeName = ubuntu-mono-dark
real transparency on... depth: 32
panel items: TSC
Systray composited rendering on
tint2 : nb monitor 2, nb monitor used 2, nb desktop 2
Kernel uevent interface initialized...

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

Title:
  Windows change Monitor/Desktop after screen lock

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