I've set a folder to sync, which has two subfolders, each of which has many subfolders as well. The main directory (the one I've set to sync) has synced onto my other computer but is devoid of its contents. I've never had this problem before.
This looks like a bug LP:869920 we are currently working on. The synchronization will work correctly when you restart the client completely (e.g. with the following in the terminal):
u1sdtool --quit u1sdtool --start