you have org.gnome.Nautilus.desktop in that config which is correct, do
you have a local nautilus .desktop in .local/share/applications? how do
you start it? do you get the issue in a guest session?

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https://bugs.launchpad.net/bugs/1448764

Title:
  Nautilus opens as a different app

Status in nautilus package in Ubuntu:
  Incomplete

Bug description:
  I'm sorry if this is just a very small bug, it really annoys me.
  I have Nautilus locked on my Launcher. When I click on its icon, nautilus 
should be "attached" to that icon.
  However, it opens at the bottom like a different application (look at image 
for example).
  Thanks in advance
  William

  ProblemType: Bug
  DistroRelease: Ubuntu 15.04
  Package: nautilus 1:3.14.2-0ubuntu9
  ProcVersionSignature: Ubuntu 3.16.0-28.38-generic 3.16.7-ckt1
  Uname: Linux 3.16.0-28-generic x86_64
  ApportVersion: 2.17.2-0ubuntu1
  Architecture: amd64
  CurrentDesktop: Unity
  Date: Sun Apr 26 20:41:55 2015
  GsettingsChanges:
   b'org.gnome.nautilus.list-view' b'default-visible-columns' b"['name', 
'size', 'type', 'date_modified', 'mime_type']"
   b'org.gnome.nautilus.list-view' b'use-tree-view' b'true'
   b'org.gnome.nautilus.list-view' b'default-column-order' b"['name', 'size', 
'type', 'date_modified', 'owner', 'group', 'permissions', 'mime_type', 'where', 
'date_accessed']"
  InstallationDate: Installed on 2014-09-06 (232 days ago)
  InstallationMedia: Ubuntu 13.10 "Saucy Salamander" - Release amd64 
(20131016.1)
  SourcePackage: nautilus
  UpgradeStatus: Upgraded to vivid on 2015-04-23 (3 days ago)

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