Partial classes in different namespace are not being recognized correctly

You cannot have a partial class in two different namespaces. The compiler treats those as two different classes.

I have a partial that is split over two namespaces.

You can't. By being in different namespaces, they are different classes.

Consider that this is the reason namespaces exist - so you can have the same class name for different classes.

From the C# Language Specification (C# 4.0), §10.2, Partial types:

Each part of a partial type declaration must include a partial modifier. It must have the same name and be declared in the same namespace or type declaration as the other parts.

(emphasis mine)

So, by definition, what you are doing is not a partial type.

See Partial Class Definitions

Using the partial keyword indicates that other parts of the class, struct, or interface can be defined within the namespace.

This is due to the fact that partial types must be within the same namespace because each class has a fully quantified name which includes the namespace. A prime example of this is with Windows Forms Application the designer and the UI code are seperated using a partial class. It also prevents bad design in my opinion!

You can see this for yourself using simple reflection code (for fun mostly).

var namespaces = Assembly.GetExecutingAssembly().GetTypes()
                         .Select(t => t.Namespace)
                         .Distinct();

//Returns:
//  WindowsFormsApplication2
//  WindowsFormsApplication2.Properties