Just to chime in, running 16.04.2 LTS on a Lenovo E540.
I had this behaviour in dual head operation with an external full hd display.
I recently changed to a pivot QHD display, that operates in portrait mode.
I am losing windows frequently after returning from a locked screen.
This is a rather annoying and repeatable behaviour:
- I open a few applications, say, thunderbird, firefox and a terminal
- I need to leave, activate screen lock
- I return, unlock
- thunderbird window is lost, the dot is still displayed in unity's dock
- the window dows not return when clicking the application icon
- only solution is to right-click the icon, close the app and re-open it

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

Title:
  Windows change Monitor/Desktop after screen lock

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