On a closer look I don't see any big issue here. I happened to choose the only 
filetype as a test/example that *I've found*  to be an issue - .mp4
When one uses ..Details > Default, ect on video there are these 2 lines 
concerning .mp4 created - 
video/mp4=
video/mp4v-es=

So when both lines exist with a = of player A then nautilus > properties > open 
with doesn't work properly on a  .mp4 when trying to set one or the other to 
player B as default 
mimeapps.list will reflect the change but nautilus will not until the other 
line is either removed or edited to match
( most users will only have video/mp4 files..

So I guess this is a valid bug, albeit small, if would be good to know
if there are any other 'conflicts'  in video or audio mimes before
considering an upstream bug.

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https://bugs.launchpad.net/bugs/1280794

Title:
  Can't change default "Open with" application

Status in “nautilus” package in Ubuntu:
  New

Bug description:
  I am on Ubuntu 13.10 using nautilus  1:3.8.2-0ubuntu2.2.

  I am trying to change default application to open .avi files. I right-
  click an .avi file select "Properties", go to "Open With". There is a
  default application there (banshee) and recommended (VLC media
  player). I select VLC media player and click "Set as default" button,
  selection jumps back to banshee, "Set as default" button disabled and
  nothing else happens. Nautilus still opens .avi files with banshee.

  ProblemType: Bug
  DistroRelease: Ubuntu 13.10
  Package: nautilus 1:3.8.2-0ubuntu2.2
  ProcVersionSignature: Ubuntu 3.11.0-15.25-generic 3.11.10
  Uname: Linux 3.11.0-15-generic x86_64
  ApportVersion: 2.12.5-0ubuntu2.2
  Architecture: amd64
  Date: Sun Feb 16 21:45:45 2014
  GsettingsChanges: b'org.gnome.nautilus.window-state' b'geometry' 
b"'1497x873+0+171'"
  InstallationDate: Installed on 2013-11-17 (91 days ago)
  InstallationMedia: Ubuntu 13.10 "Saucy Salamander" - Release amd64 
(20131016.1)
  MarkForUpload: True
  SourcePackage: nautilus
  UpgradeStatus: No upgrade log present (probably fresh install)
  mtime.conffile..etc.xdg.autostart.nautilus.autostart.desktop: 
2013-11-20T19:34:55.419627

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