Similar problem here. BTsync 2 is too complicated and not very flexible. I am now running an 1.4 on all devices, I had to downgrade them. I will take a look at owncloud. btsync 2 had also the bug then adding a folder with subfolders. A dialog appeared asking if I want to add the subfolders but I couldn't get rid of this message and finally I wasn't able to add this folder.