You have to perform deep diagnostic by yourself, because the question under consideration requires the source code to be published here. It also can depend on the environment where the script is running, in order to get you the right answer.
You have an option on MSBuild utility to pass verbosity level of output. Use the following switch value to get detailed information about how the references are resolved during the build:
msbuild ./Source/My.Project.sln /t:Build /v:d
Using this command, you can navigate to the steps called ResolveAssemblyReference and ResolveProjectReference. You can see all the paths, where it will search for assemblies, and if it is succeded:
4> Primary reference "System.Runtime.Remoting, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089".
4> Resolved file path is "C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\System.Runtime.Remoting.dll".
4> Reference found at search path location "{TargetFrameworkDirectory}".
4> For SearchPath "C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\atlmfc\lib\amd64".
4> Considered "C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\atlmfc\lib\amd64\System.Runtime.Remoting.winmd", but it didn't exist.
4> Considered "C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\atlmfc\lib\amd64\System.Runtime.Remoting.dll", but it didn't exist.
4> Considered "C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\atlmfc\lib\amd64\System.Runtime.Remoting.exe", but it didn't exist.
4> For SearchPath "C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\lib\amd64".
4> Considered "C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\lib\amd64\System.Runtime.Remoting.winmd", but it didn't exist.
4> Considered "C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\lib\amd64\System.Runtime.Remoting.dll", but it didn't exist.
4> Considered "C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\lib\amd64\System.Runtime.Remoting.exe", but it didn't exist.
4> For SearchPath "{TargetFrameworkDirectory}".
4> Considered "C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\System.Runtime.Remoting.winmd", but it didn't exist.
4> This reference is not "CopyLocal" because it's a prerequisite file.
4> The ImageRuntimeVersion for this reference is "v4.0.30319".
You also can examine which references were passed to the compiler if you look at commandline, which was generated by MSBuild and find out if there is a reference you are required in.
For cl:
4> C:\Program Files (x86)\Microsoft Visual Studio 10.0\VC\bin\x86_amd64\CL.exe
...
/AI"C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0"
...
/FU"C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\mscorlib.dll"
/FUE:\YourProj\bin\Debug\Your.Proj.dll
/FU"C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\System.Configuration.dll"
...
/errorReport:prompt
YourSourceCodeFiles.cpp
/clr:nostdlib
For csc:
2> C:\Program Files (x86)\MSBuild\12.0\bin\Csc.exe
...
/reference:"C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\Profile\Client\mscorlib.dll"
/reference:E:\svn\PRM\trunk\PRM30\bin\Debug\Prm.Base.dll
/reference:"C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\Profile\Client\System.Configuration.dll"
/reference:"C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.0\Profile\Client\System.Core.dll"
...
(most of parameters were omited for simplicity)