Hi Dan,
Maybe the difference with us is that I only register the custom content type on a subfolder under the root. Not on the root itself. I believe you won't be able to put a content folder unless that content type is registered on that folder or its parents.
Anyway I will try to register my custom content type on the root (-100). If that fails I will post a script here. My pg db is kinda screwed now with all the experimentation done on it. I think it would best to start from a fresh install, also that way we eliminate some of the variables.
I will post as soon as I can.