Subsequent packaging attempts fail when packaging with Chunks, Nativization, Full Rebuild and For Distribution enabled

Subsequent packaging attempts when Generate Chunks, Blueprint Nativization, Full Rebuild, and For Distribution are enabled will fail. The error that appears states that the AutomationTool log file is being used by another process and therefore cannot be written to.

Project: [Link Removed]

Error:

[2017.05.04-21.13.51:883][869]UATHelper: Packaging (Windows (64-bit)): Program.Main: ERROR: AutomationTool terminated with exception: System.AggregateException: One or more errors occurred. ---> AutomationTool.AutomationException: Failed to Write to file C:\Users\matthew.clark\AppData\Roaming\Unreal Engine\AutomationTool\Logs\D+Epic+Games+4.15\UnrealPak-2017.05.04-17.13.50.txt ---> System.IO.IOException: The process cannot access the file 'C:\Users\matthew.clark\AppData\Roaming\Unreal Engine\AutomationTool\Logs\D+Epic+Games+4.15\UnrealPak-2017.05.04-17.13.50.txt' because it is being used by another process.

Regression?: No
This also occurred in 4.14

1. Download the project in the description
2. Generate project files, compile, and open the project
3. Package the project
4. After the packaging attempt completes, package again
   Result: The packaging attempt fails with the error listed in the description
   Expected: The packaging attempt succeeds