Public bug reported:

On Ubuntu 16.04.2: After installing xpdf it was not listed in the "Other
Applications" list in "properties" -> "Open With" dialogue of a file.

So this may imply that there are multiple places managing the filetype
<-> application relation.

I had "PDF Mod" set as default appliction for pdf. After removing it
from "Open With" -> "Other Application..." -> "Related Application" xpdf
appeared in "properties" -> "Open With" -> "Default Apllication" but not
in "Open With" -> "Other Application..." -> "Related Applications". In
the first row of the right-click menu of the pdf-file the listed default
application changed randomly between xpdf and something else.

Clicking "Set as default" in the "properties" -> "Open With" after
selecting one application let the xpdf disapear, unable to reselect it.

My other nautilus bug reports may be related to this.

ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: nautilus 1:3.18.4.is.3.14.3-0ubuntu5
ProcVersionSignature: Ubuntu 4.4.0-72.93-generic 4.4.49
Uname: Linux 4.4.0-72-generic x86_64
NonfreeKernelModules: nvidia_uvm nvidia_drm nvidia_modeset nvidia
ApportVersion: 2.20.1-0ubuntu2.5
Architecture: amd64
CurrentDesktop: Unity
Date: Tue May  2 00:58:14 2017
GsettingsChanges:
 b'org.gnome.nautilus.window-state' b'sidebar-width' b'253'
 b'org.gnome.nautilus.window-state' b'geometry' b"'890x522+1030+530'"
SourcePackage: nautilus
UpgradeStatus: No upgrade log present (probably fresh install)

** Affects: nautilus (Ubuntu)
     Importance: Undecided
         Status: New


** Tags: amd64 apport-bug xenial

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https://bugs.launchpad.net/bugs/1687497

Title:
  multiple default application settings conflicting

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