Jenkins build not installing scenes

I'm currently attempting to setup an automated Jenkins build of a Unity 5.4.1f1 project on a Windows server.

Attached is the buildscript I'm calling from the command line with the command:

 "C:\Program Files\Unity\Editor\Unity.exe" -batchmode -quit -executeMethod BuildScript.PerformWindows64Build  -projectPath "<SuperImportantProjectPath>" -logFile "<SuperImportantProjectPath>\SuperImportantProject.log"

If I build this on the server using the GUI Build Settings it builds fine. If I build it through the menu created by the build script it builds fine. If I build it from the command line it builds fine. If I build it in Jenkins, whether via a batch command or the Unity3d plugin, it fails to load any scenes when you attempt to run it.

The logs for the successful vs unsuccessful are exactly the same until these lines appear in the unsuccessful output log:

 (Filename: C:/buildslave/unity/build/artifacts/generated/common/runtime/UnityEngineDebugBindings.gen.cpp Line: 42)
 
 No downloadData scenes in CurrentApplicationInfo. Cancelling load...
  
 (Filename: C:/buildslave/unity/build/artifacts/generated/common/runtime/UnityEngineDebugBindings.gen.cpp Line: 42)
 
 DontDestroyOnLoad only work for root GameObjects or components on root GameObjects.
  
 (Filename:  Line: 386)

I've included the full log file here.

I accept this is a problem with jenkins rather than Unity, but does anybody have any idea what I'm doing wrong?