Changing project settings in the Editor can result in duplicate entries in the project's .ini files.

Changing the packaging settings for a project in the Editor results in double entries in the .ini file for the project.

This seems to have worked fine in 4.5.1 (CL 2336109). Found broken in 4.6.1 (CL 2389353) and Main (CL 2391021).

1. Create a new blueprint project using the first person template.
2. Locate the DefaultGame.ini file for the project and open it.
   • The file will display something similar to the following:

     [/Script/EngineSettings.GeneralProjectSettings]
     ProjectID=2AF8F00B41954572A9BAC480B03ADEFE
     ProjectName=First Person BP Game Template
     

3. Close the DefaultGame.ini file.
4. Open the Packaging Settings for the project
   • File -> Package Project -> Packaging Settings
5. In the Packaging section, change each of the four default values.
6. Close the Editor.
7. Open the DefaultGame.ini file again.
   • It now will show something similar to the following:

     [/Script/EngineSettings.GeneralProjectSettings]
     ProjectID=2AF8F00B41954572A9BAC480B03ADEFE
     ProjectName=First Person BP Game Template
     
     [/Script/UnrealEd.ProjectPackagingSettings]
     StagingDirectory=(Path=)
     ForDistribution=False
     UsePakFile=True
     UsePakFile=False
     bGenerateChunks=False
     bGenerateChunks=True
     IncludePrerequisites=True
     IncludePrerequisites=False
     UseOBB_InAPK=False
     UseOBB_InAPK=True
     +CulturesToStage=en
     

RESULT:
Some of the settings have duplicate entries in the .ini file that set the default value for that setting, then immediately set the value that it was changed to.

EXPECTED:
Only one entry appears for each setting, changing it to the value it was set to in the Editor.

What is going on with duplications in .ini files?