Hello,
The first mass balance is from Telemac-2D, the second is from Sisyphe. Only the message from Telemac-2D seems to report an error. Some hints:
1) Did you ask for : CONTINUITY CORRECTION = YES
2) Do you have a mass conservative advection scheme for tracers, i.e. not characteristics (1).
3) Do you have tidal flats ? (in which case only advection scheme 13 or 14 (the same) would work ?
4) Do you have a large diffusion coefficient ? (if yes try with coefficient =0.)
5) Did you ask for OPTION FOR FLUXES AT THE BOUNDARIES = 2;2;2... (not sure of the name of this keyword, I'm on holidays with (and exceptionnally today) little Internet connection).
With best regards,
Jean-Michel