There are several reasons of your observation, being the most simple one the discretization. If you would like to improve the vertical moisture profile in the unsaturated zone, you basically need to work with more slices.
Also, FEFLOW does not apply directly the recharge to the water table. The fact that you are solving the Richards eq., FEFLOW is capable to simulate the propagation of the wetting front (let's say from top surface) down to the water table. If you are getting less recharge, then it may be you need to improve parameter settings (conductivity, unsaturated param. etc).
Cheers
Carlos
