We use an internal tool to build our help, similar to NDoc although we have a lot of extra features in it. Such as the ability to write other topics, design a TOC, and merge it with the class library documentation. It also uses SyntaxEditor to generate highlighted code.
We just fixed the topic not found problem when linking to framework classes. The fixes should appear in the next maintenance releases.
I hadn't heard of the Sandcastle product before. It looks promising. Perhaps we could somehow swap its engine into our documentation building application. Then have the best of both worlds. :)