Hello,
First thing, Fudaa just helps you to fill the parameter file, you can bypass it and edit this file directly, and run the program without Fudaa, but your problems seems to come from the fact that you impose the depth at the entrance in a fluvial flow. You must relax the depth (4 5 5 in the boundary conditions file), but an important thing is the initial conditions, you must have water at boundaries where you impose a discharge.
As you probably also impose the depth or elevation at the exit, you will not see the correct discharge at the exit in the listing unless you use :
CONTINUITY CORRECTION : YES
in the parameter file (because the equation h = imposed depth replaces the continuity equation, and we need to take care of that).
I hope this helps,
Jean-Michel Hervouet