Hello. I have experienced this bug after updating from Ubuntu 14 to Ubuntu 16 
(it did not exist in Ubuntu 14).
Following what it is said in this thread, I have created an script in $HOME/bin 
with the contents:

gnome-session-quit --logout --no-prompt

To logout, I open a terminal and execute this script (whit a shorter
name and easier to remember than the full command). As previously told,
it only works if no attempt to logout by other method has been issued
before. Perhaps a button in the dock associated to this script might be
created to make things easier (how???)

For me, the bug exist if the session is open with cairo-dock but not if
it is open with plain metacity.

If the problem is just a dialogue box not appearing, at is seems, why is
that difficult to solve this bug which seems to survive through several
Ubuntu updates?

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https://bugs.launchpad.net/bugs/1448418

Title:
  Logout not working in Cairo Dock

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