I’m having issues with packaging as well, both 64 and 32 bit. I get the following output:
UATHelper: Packaging (Windows (64-bit)): Project.Build: ********** BUILD COMMAND STARTED **********
UATHelper: Packaging (Windows (64-bit)): CommandUtils.Run: Run: C:\Program Files (x86)\Epic Games\4.13\Engine\Binaries\DotNET\UnrealBuildTool.exe FS Win64 Development -Project=C:\... C:\... -remoteini="C:\..." -noxge -generatemanifest -NoHotReload
UATHelper: Packaging (Windows (64-bit)): UnrealBuildTool: Performing full C++ include scan (building a new target)
UATHelper: Packaging (Windows (64-bit)): UnrealBuildTool: Messages while compiling C:\Program Files (x86)\Epic Games\4.13\Engine\Intermediate\Build\BuildRules\UE4Rules.dll:
UATHelper: Packaging (Windows (64-bit)): UnrealBuildTool: c:\Program Files (x86)\Epic Games\4.13\Engine\Plugins\TrueSkyPlugin\Source\TrueSkyEditorPlugin\TrueSkyEditorPlugin.Build.cs(5,15) : error CS0101: The namespace 'UnrealBuildTool.Rules' already contains a definition for 'TrueSkyEditorPlugin'
UATHelper: Packaging (Windows (64-bit)): UnrealBuildTool: c:\Program Files (x86)\Epic Games\4.13\Engine\Plugins\TrueSkyPlugin\Source\TrueSkyPlugin\TrueSkyPlugin.Build.cs(5,15) : error CS0101: The namespace 'UnrealBuildTool.Rules' already contains a definition for 'TrueSkyPlugin'
UATHelper: Packaging (Windows (64-bit)): UnrealBuildTool: ERROR: UnrealBuildTool encountered an error while compiling source files
UATHelper: Packaging (Windows (64-bit)): CommandUtils.Run: Run: Took 0.5483438s to run UnrealBuildTool.exe, ExitCode=5
UATHelper: Packaging (Windows (64-bit)): Program.Main: ERROR: AutomationTool terminated with exception: AutomationTool.CommandUtils+CommandFailedException: Command failed (Result:5): C:\Program Files (x86)\Epic Games\4.13\Engine\Binaries\DotNET\UnrealBuildTool.exe FS Win64 Development -Project=C:
UATHelper: Packaging (Windows (64-bit)): \... C:\... -remoteini="C:\..." -noxge -generatemanifest -NoHotReload. See logfile for details: 'UnrealBuildTool-2016.10.23-14.00.11.txt'