I ran into this situation today. I have an object which I'm testing for equality; the Create() method returns a subclass implementation of MyObject.
MyObject a = MyObject.Create();
MyObject b = MyObject.Create();
a == b; // is false
a.Equals(b); // is true
Note I have also over-ridden Equals() in the subclass implementation, which does a very basic check to see whether or not the passed-in object is null and is of the subclass's type. If both those conditions are met, the objects are deemed to be equal.
The other slightly odd thing is that my unit test suite does some tests similar to
Assert.AreEqual(MyObject.Create(), MyObject.Create()); // Green bar
and the expected result is observed. Therefore I guess that NUnit uses a.Equals(b) under the covers, rather than a == b as I had assumed.
Side note: I program in a mixture of .NET and Java, so I might be mixing up my expectations/assumptions here. I thought, however, that a == b worked more consistently in .NET than it did in Java where you often have to use equals() to test equality.
UPDATE Here's the implementation of Equals(), as requested:
public override bool Equals(object obj) {
return obj != null && obj is MyObjectSubclass;
}