You have a Visual Studio 2010 project that creates an installer for a native VC++ application. The application does not require the .NET Framework to be installed. After installing .NET 4.5 (or Visual Studio 2012, which installs .NET 4.5), you observe that your VS 2010 Setup project now has a dependency on the .NET Framework.
A managed assembly is being incorrectly added to the list of references for the native project, causing the native project to have a dependency on the .NET Framework.
The "AddAdditionalExplicitAssemblyReferences" property needs to be set to false for the VC++ project. One direct way to accomplish this would be to edit the .vcxproj file to do so. Before editing the .vcxproj, ensure that you do not have the project opened in any Visual Studio instances. With an XML or text editor (such as the one in Visual Studio), you will observe that the .vcxproj begins something like this: