It works as expected after last update.

** Changed in: software-center (Ubuntu)
       Status: Confirmed => Fix Released

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https://bugs.launchpad.net/bugs/1292613

Title:
  "New Application in launcher" option change is not persistance

Status in “software-center” package in Ubuntu:
  Fix Released

Bug description:
  "New Application in launcher" option restore (checked) after restart
  software-center.

  Expected: If i uncheck any option, it should remain uncheck after
  restart software-center even after restart the system

  Currently: "New Application in launcher" settings restore as checked.

  ProblemType: Bug
  DistroRelease: Ubuntu 13.10
  Package: software-center 13.10-0ubuntu1
  Uname: Linux 3.12.6-031206-generic x86_64
  ApportVersion: 2.12.5-0ubuntu2.2
  Architecture: amd64
  Date: Fri Mar 14 22:45:53 2014
  ExecutablePath: /usr/share/software-center/software-center
  InterpreterPath: /usr/bin/python2.7
  MarkForUpload: True
  PackageArchitecture: all
  ProcEnviron:
   LANGUAGE=en_US
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=en_US.UTF-8
   SHELL=/bin/bash
  SourcePackage: software-center
  UpgradeStatus: No upgrade log present (probably fresh install)

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