I often see the following error during packaging:
LogPlayLevel: Program.Main: ERROR: AutomationTool terminated with exception: AutomationTool.AutomationException: Failed to delete file 'C:\UnrealEngine\Engine\Binaries\DotNET\UnrealBuildTool.exe'
The file is not write protected and as far as I can see has no special permissions set (running windows 7).