Hello Stephen,
To have a chance to see an exact mass balance, you need to have the keyword:
CONTINUITY CORRECTION : YES
in your steering file. It must be so because at your exit the continuity equation is replaced by the equation prescribing the elevation, so the exiting flux computed with the velocities at the exit may not be compatible with continuity. CONTINUITY CORRECTION forces the compatibility.
You will find a mass balance of the order of magnitude of the accuracy asked for propagation. Then if you use TREATMENT OF NEGATIVE DEPTHS = 2 you will find the accuracy of the machine, because this options recomputes the continuity in an exact way.
With best regards,
Jean-Michel Hervouet