EDIT: This may not technically be a bug, although some additional functionality could be added to avoid the situation. I had another class with the exact same name as the namespace. This kept the XAML compiler from correctly finding the classes. A warning should probably be thrown that naming a class the same as its namespace is not recommended.
Using custom XAML objects, with associated code behind, both were set up to inherit to Option.cs, and then Option.cs was set to inheir to UserControl. The root object of the XAML refused to recognize the Option.cs class. The namespaces were defined correctly. I attempted to put the entire project into Class Library starup mode with no success. I put the Option.cs file into another assembly and it worked flawlessly. I imported the exact same project into MS VS 2010 and it also worked flawlessly.