How do I get my proposed terrain to show up in the same view window as my cross section and my vertical alignment?

Thanks. I think that was the problem.

You may be seeing this if you have a 3D Cut in a profile view. Either refresh the 3D Cut or delete it if you don't need it anymore, and that warning will likely go away. 

That looks like that Default-3D model is attached twice. Since that's the reference dialog, you don't have two models with the same name, you have one model attached two times.

And I have no idea why, but every time I go from my 3D model to my Default model, all of the view windows except view 1 and view 2 (which shows up blank) vanish, and I have to set up the views again.

It doesn't look like there's anything in my 3D file, which is weird because the references are referenced in and turned on. It's not usually like this. This is seems like a weird problem.