This bug was fixed in the package ubuntu-mate-settings - 16.10.0

---------------
ubuntu-mate-settings (16.10.0) yakkety; urgency=medium

  * Do not automatically start Tilda.
  * Migrate to LibreOffice Tango icons.
  * Hide Compton desktop icon when running MATE.

 -- Martin Wimpress <c...@flexion.org>  Tue, 17 May 2016 22:57:48 +0100

** Changed in: ubuntu-mate-settings (Ubuntu)
       Status: Fix Committed => Fix Released

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https://bugs.launchpad.net/bugs/1574789

Title:
  xorg.conf.d/90-zap.conf destroys xorg keyboard settings

Status in ubuntu-mate:
  Fix Committed
Status in ubuntu-mate-settings package in Ubuntu:
  Fix Released
Status in ubuntu-mate-settings source package in Xenial:
  Fix Committed

Bug description:
  With Ubuntu MATE 16.04, I'm unable to switch between keyboard layouts
  properly.

  My locale is LANG=el_GR.UTF-8 and LANGUAGE=el.
  The Ubuntu MATE installer correctly made those settings for me:
  $ grep -i xkboptions /etc/default/keyboard
  XKBOPTIONS="grp:alt_shift_toggle,grp_led:scroll"

  I.e. I should be able to switch between the US and the Greek keyboard
  layout using Alt+Shift, and the keyboard scroll led indicates the
  active language.

  Unfortunately ubuntu-mate-default-settings overrides the correct
  settings, making me unable to switch languages via Alt+Shift:

  $ grep -i xkboptions /usr/share/X11/xorg.conf.d/90-zap.conf
      Option "XKbOptions" "terminate:ctrl_alt_bksp,grp"

  So, please make sure that 90-zap.conf *adds* "terminate:ctrl_alt_bksp,grp" to 
the current xkboptions, instead of *replacing* them.
  If it's unable to add instead of replacing settings, then please completely 
remove 90-zap.conf.

  [Impact]

   * Ubuntu MATE included the ability to kill the X server using
  Ctrl+Alt+BkSpc over a year ago while the initial Compiz integration
  was being added. That facility is a hangover and no longer required.

   * This updated version of Ubuntu MATE Settings removes
  usr/share/X11/xorg.conf.d/90-zap.conf and restores the ability to
  switch keyboard layouts using Alt+Shift.

  [Test Cases]

   * Install Ubuntu MATE 16.04 using Greek language and locale and US
  language. You will be unable to switch between the US and the Greek
  keyboard layout using Alt+Shift.

   * Once Ubuntu MATE Settings 16.04.5.1 is installed it will be
  possible to switch between keyboard layouts using Alt+Shift.

  [Regression Potential]

   * The ability to kill the X session using Ctrl+Alt+BkSpc will be
  lost. But none of the other Ubuntu flavours support this functionality
  and it's removal restore the default Xorg behaviour.

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