Sounds like a Qt issue (similar to #1637020).

** Package changed: vlc (Ubuntu) => qtbase-opensource-src (Ubuntu)

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https://bugs.launchpad.net/bugs/1637034

Title:
  Ubuntu Mate 16.04 mouse inputs not handled correctly on multi gpu
  system

Status in ubuntu-mate:
  Invalid
Status in dolphin package in Ubuntu:
  New
Status in qtbase-opensource-src package in Ubuntu:
  New

Bug description:
  
    My mouse inputs aren't being handled properly by a few but not all 
applications in Ubuntu 16.04 using the Mate desktop.  The problem occurs on my 
system that has 3 gpus, 5 monitor setup with compiz, accelerated graphics, and 
xinerama enabled.  I'm using the Nvidia 361 drivers.  I do not have these 
problems on my laptop, a single monitor setup with compiz and accelerated 
graphics enabled.

    Applications like the Caja file manager handles all the mouse inputs
  correctly, but the Dolphin file manager doesn't.  In Dolphin, I can
  mouse click the menu items just fine, but any sub-menu mouse inputs
  are not registered.  Also in Dolphin, none of the mouse inputs are
  recognized while clicking on any of the files/folders/places but I can
  still use the mouse to scroll the file list window.

    Other applications that exhibit this odd mouse behavior are VLC and
  SMPlayer (see https://bugs.launchpad.net/ubuntu-mate/+bug/1637020 for
  a bug with VLC that I filed that I believe has a similar root cause).
  Other applications that I've used that don't exhibit this behavior are
  firefox, chromium, virtual box kaffeine, tvtime...  actually, all the
  other programs I've tried don't have this problem.  I'll update the
  list of problem applications as I come across them.  My *guess* is
  that the common denominator between these problem applications is that
  they use the same graphical tool kit and that there is a flaw in that
  tool kit's implementation that affects multi-gpu systems.

    If you want, I can record my desktop to demonstrate the problem.

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