Hello,
You can check first on the listing that the solver for the diffusion of tracers always does at least 1 iteration, if not increase the accuracy, but it is already 1.D-12, so probably enough. A most probable reason is the OPTION FOR THE DIFFUSION OF TRACERS which perhaps causes trouble or differences of propagation on shallow zones, try 1 instead of 2 and see what happens. It is true that in theory we should not simplify the depth across the derivative, but in practice the diffusion in a depth-averaged context also contains the dispersion due to the heterogeneity of velocity on a vertical, which sometimes is even not treated as a diffusion but as an advection, so we have a lot of uncertainty here.
With best regards,
Jean-Michel Hervouet