I've the exact same problem. Alfred will find (using any of the File Search keywords) files & folders at deep levels inside my user folders, documents, downloads, etc.
But the DropBox folder... Alfred seems to stop at level 3 (eg. ~/Dropbox/Folder1/Folder2/Folder3 but doesn't find files nor folders inside Folder3).
Like the OP, I tried adding the ~/Dropbox folder to the Search Scope.
And like the OP, Spotlight finds stuff in the full Dropbox folder system as expected.