What happens if you right-click on one of the photos in your smart-collection and then select Go To Folder in Library? Does the photo appear in the highlighted folder in the Folder Panel? (you might have to scroll up or down to find the highlighted folder) Is that the proper folder it should be in?
Yes! That worked! Should I do that with each of my folders? The pictures are in a sub-folder called RAW files and the main folder still says 0 photos - is there a reason for that?
To tell you the truth, I have no idea why you are seeing what you are seeing, or what your Folder Panel in Lightroom looks like, but if it works, you can keep doing it.
Maybe you could show us a screen capture of the Folder Panel in Lightroom.