I get a different C# object instance when calling the constructor from reflection

Compare the two instances of the same class below. The variable instanceA is created using reflection, while instanceB is created using a direct reference to the DLL from my VS2012 project.

var a = Assembly.Load(File.ReadAllBytes(@"C:\MyFilePath.dll"));
var t = a.GetType("Namespace.MyClassType");

var instanceA = Activator.CreateInstance(t);
var instanceB = new Namespace.MyClassType();

The problem? These are not equal. The fields in instanceA and instanceB are different. Currently my code is working, as long as I'm using instanceB. But if I change only the letter "B" to "A" then the resulting object is somewhat different which in a later stage breaks the product.

As you probably understand, my task is to use reflection instead of a reference. I have confirmed that the correct constructor is being called.