Two things here, the "size on disk" value for folders as displayed in Windows has been wrong for ages already on this model, so ignore that. For actual space used go with NasNavigator or the LinkStation GUI.
As for the LinkStation actually being full in this case: check your trashbox. Are those automated backups running to the LinkStation (i.e. some kind of backup program is used)? If so make sure the trashbox is deactivated for that share folder.