I think maybe I know what is happening. When you do a partial sync, it will not populate the folders with tracks of subplaylists, unless a folder is specifically selected to be synced.
Because when you have something like this:
Folder
Playlist A
Playlist B
And you select only A, then the folder can’t be given all tracks because B was not synced as well.
On a full sync, the folders should contain all child tracks.