As discussed via e-mail, Boxifier was syncing correctly.
The confusion was probably due tot the shortcuts placed in the Boxifier folder.
We initially thought of those shortcuts as placeholders so that one could easily jump to the original locations.
In the last months we came to the conclusion that those are somehow confusing for some of our users (some simply believe that Boxifier would be using shortcuts to do the sync process - which is not true) and we are thinking of removing those shortcuts in the future.