Looks like this commit fixes it:

revno: 2327
committer: Robert Ancell <robert.anc...@canonical.com>
branch nick: 1.18
timestamp: Wed 2016-06-29 15:16:05 +1200
message:
  Remove unused unititialized file descriptors - could cause stdin to be closed

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https://bugs.launchpad.net/bugs/1605117

Title:
  LightDM tray items disappear after logout

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