I have four projects in my Visual Studio solution (everyone targeting .NET 3.5) - for my problem only these two are important:
I'm not sure why it is different when building between Visual Studio and MsBuild, but here is what I have found when I've encountered this problem in MsBuild and Visual Studio.
For a sample scenario let's say we have project X, assembly A, and assembly B. Assembly A references assembly B, so project X includes a reference to both A and B. Also, project X includes code that references assembly A (e.g. A.SomeFunction()). Now, you create a new project Y which references project X.
So the dependency chain looks like this: Y => X => A => B
Visual Studio / MSBuild tries to be smart and only bring references over into project Y that it detects as being required by project X; it does this to avoid reference pollution in project Y. The problem is, since project X doesn't actually contain any code that explicitly uses assembly B (e.g. B.SomeFunction()), VS/MSBuild doesn't detect that B is required by X, and thus doesn't copy it over into project Y's bin directory; it only copies the X and A assemblies.
You have two options to solve this problem, both of which will result in assembly B being copied to project Y's bin directory:
Personally I prefer option 2 for a couple reasons.
Here is a sample of the "dummy code" that I typically add when I encounter this situation.
// DO NOT DELETE THIS CODE UNLESS WE NO LONGER REQUIRE ASSEMBLY A!!!
private void DummyFunctionToMakeSureReferencesGetCopiedProperly_DO_NOT_DELETE_THIS_CODE()
{
// Assembly A is used by this file, and that assembly depends on assembly B,
// but this project does not have any code that explicitly references assembly B. Therefore, when another project references
// this project, this project's assembly and the assembly A get copied to the project's bin directory, but not
// assembly B. So in order to get the required assembly B copied over, we add some dummy code here (that never
// gets called) that references assembly B; this will flag VS/MSBuild to copy the required assembly B over as well.
var dummyType = typeof(B.SomeClass);
Console.WriteLine(dummyType.FullName);
}