The short answer is that if you install a NuGet package from Visual Studio (either using PowerShell or the dialog), any assemblies that it contains will be referenced from the Packages folder.

Note that Visual Studio has some quirky behavior such that if you try to build and the packages folder is missing, and the DLL file exists in the 'bin' folder, then it switches the reference to go to the 'bin' folder. Maybe that's what you are seeing?

If that's not the case, and you have a reproducible set of steps that lead to assemblies being referenced not from the Packages folder, please open a bug on http://nuget.codeplex.com/.