Hello Sven,
Sure it is the reason. To run the NERD scheme (13-14) you need to have the fluxes between points computed by Telemac-2D or 3D. Generally speaking to have a conservative advection when solving the non-conservative form of the advection equation you need to have the discrete continuity equation available (old and new depths, fluxes between points). This is not possible in stand-alone mode, especially if you do not keep the same time-step. Furthermore, in standalone mode Sisyphe updates the velocities with somewhat wrong assumptions (e.g. considering that the product h*u will remain constant). This latter approximation may produce strange patterns of sedimentation, which are totally artificial. This is why we think that we should stop the standalone mode and do not recommend it.
This does not explain why you seem to have good results with scheme 4. With this latter scheme, which does not work with tidal flats I programmed an option in the case where the velocity field does not obey the continuity equation. This saves mass conservation but spoils the monotonicity. This option is also used when there is a velocity correction in Sisyphe, to take into account the fact that the sediment "sees" the velocity near the bottom.
With best regards,
Jean-Michel Hervouet