Hi Carl
Same problem with (AS3 Loaders + Document Class Instantiation), this seems like a flash bug to me, deeply nested clips won't appear if they are instantiated using document classes, however they exist in memory and are responding to function calls.
Everything works and displays if I don't choose the route of Document Class instantiation and instead just add the loader.content, however, this will defeat the purpose if wanna instantiate/add a loaded swf multiple times.