I recently updated to Visual Studio 2013 Update 3, but it appears as though the TypeScript compiler is a little more strict in external module compilation. If you receive an error message asking the --module flag to be set, you need to add this to your build configurations in your project:
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
<TypeScriptModuleKind>amd</TypeScriptModuleKind>
</PropertyGroup>
<PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
<TypeScriptModuleKind>amd</TypeScriptModuleKind>
</PropertyGroup>
After adding the TypeScriptModule kind node to the project properties, the compiler can correctly compile external TypeScript modules!