Hello Nicolas,
Have you tried to decrease your time step, e.g. 0.5 s rather than 1 s (or even less). Do you have smoother results for low tides then or the same as 1 s?
What about the output file/listing, do you have messages like:
POSITIVE DEPTHS SOLVED IN XXX ITERATIONS = MAXIMUM
INCREASE MAXIMUM NUMBER OF ITERATIONS FOR ADVECTION SCHEMES
?
If yes, and if it often occurs, you should increase the default value of the keyword MAXIMUM NUMBER OF ITERATIONS FOR ADVECTION SCHEMES (e.g. 100 or even more).
What you describe does not surprise me if the location where you look at time series is closed to shallows or in particular tidal flats or dry areas.
When it occurs, I try to draw figures at a location a little bit farther with deeper bottom elevations to avoid a kind of capping of the low levels (or disturbances).
I do not have more advice for your steering file at the moment.
Hope this helps,
Chi-Tuan