Kyle,
What ConDoc drawing set are you using? I know that my model doesn’t always generate correctly after creating scenes. Just hit the RESET button on the systems tool bar and that should get you where you want.
If you’re model is not apperaing in the scenes then you have something(s) tagged incorrectly. For the scenes generator work objects have to be tagged with ConDoc tags. If they’re not then ConDocs wil do one of two things, hide or display in all scenes anything not tagged with a ConDoc tag. Hope that helps