Actually, I just looked at the exception message again. That code is rather stupidly designed! I'm only handling a subset of the available documentation types (types, namespaces, methods, and properties) but there are others... instead of just ignoring the others I'm stupidly throwing this exception.
Could you do me a favor and just verify what I think will be happening. If you have a look in the XML file that's being used, and do a search for E: and F: if either of those come up then that's what will be causing the exception.