The handling of nodes above the gw surface depends on the mode you're using for those: 'confined', 'free', 'phreatic', 'unsaturated'. Except for 'free', FEFLOW will calculate also hydraulic head above the GW level, and particles will thus follow the head gradient also at nodes above the surface. You should check what option you are using and what this option means for the handling of the unsaturated zone.