Using Linq Except not Working as I Thought

So just for completeness...

// Except gives you the items in the first set but not the second
    var InList1ButNotList2 = List1.Except(List2);
    var InList2ButNotList1 = List2.Except(List1);
// Intersect gives you the items that are common to both lists    
    var InBothLists = List1.Intersect(List2);

Edit: Since your lists contain objects you need to pass in an IEqualityComparer for your class... Here is what your except will look like with a sample IEqualityComparer based on made up objects... :)

// Except gives you the items in the first set but not the second
        var equalityComparer = new MyClassEqualityComparer();
        var InList1ButNotList2 = List1.Except(List2, equalityComparer);
        var InList2ButNotList1 = List2.Except(List1, equalityComparer);
// Intersect gives you the items that are common to both lists    
        var InBothLists = List1.Intersect(List2);

public class MyClass
{
    public int i;
    public int j;
}

class MyClassEqualityComparer : IEqualityComparer<MyClass>
{
    public bool Equals(MyClass x, MyClass y)
    {
        return x.i == y.i &&
               x.j == y.j;
    }

    public int GetHashCode(MyClass obj)
    {
        unchecked
        {
            if (obj == null)
                return 0;
            int hashCode = obj.i.GetHashCode();
            hashCode = (hashCode * 397) ^ obj.i.GetHashCode();
            return hashCode;
        }
    }
}

If you are storing reference types in your list, you have to make sure there is a way to compare the objects for equality. Otherwise they will be checked by comparing if they refer to same address.

You can implement IEqualityComparer<T> and send it as a parameter to Except() function. Here's a blog post you may find helpful.

edit: the original blog post link was broken and has been replaced above