I have four projects in my Visual Studio solution (everyone targeting .NET 3.5) - for my problem only these two are important:
I just ran into a very similar issue. When compiling using Visual Studio 2010, the DLL file was included in the bin folder. But when compiling using MSBuild the third-party DLL file was not included.
Very frustrating. The way I solved it was to include the NuGet reference to the package in my web project even though I'm not using it directly there.