Two immediate ideas here:
* Are the Roof Elements set to be Room Bounding? Check for this in the Element Properties dialog for the Roof Elements in question.
* Are you outputting Shading Surfaces from your model? Check for this in Settings -> Project Information -> Shading Surfaces.
Hope that helps,
Kyle B
Revit MEP Product Manager
http://inside-the-system.typepad.com/
Kyle Bernhardt
Director
Building Design Strategy
Autodesk, Inc.