You could also check to make sure the DLLs you're looking for aren't included in the GAC. I believe Visual Studio is being smart about not copying those files if it already exists in the GAC on the build machine.
I recently ran in this situation where I'd been testing an SSIS package that needed assemblies to exist in the GAC. I'd since forgotten that and was wondering why those DLLs weren't coming out during a build.
To check what's in the GAC (from a Visual Studio Developer Command Prompt):
gacutil -l
Or output to a file to make it easier to read:
gacutil -l > output.txt
notepad.exe output.txt
To remove an assembly:
gacutil -u MyProjectAssemblyName
I should also note, that once I removed the files from the GAC they were correctly output in the \bin directory after a build (Even for assemblies that were not directly referenced in the root project). This was on Visual Studio 2013 Update 5.