Hi again, I'll get back to you with more information.
After a little more investigation, I think I've put my finger on something interesting. In my first example the simulations only affected one species, whereas in the second they affected 3 species. I think that problem 1 and 2 have the same origin. When I import my csv with the simulations, it automatically writes the last simulation value to "fishing mortality functions grids". The problem is that selecting or deselecting my simulations doesn't change anything to the values displayed in "fishing mortality functions grids". So in my second example, even if I select only one simulation for a single species, there will be changes in the mortality values for all the other species, which gives me a false result. It looks like you can select simulations but deselecting them doesn't change anything in the "fishing mortality functions grids". It would therefore seem that there is no update of "fishing mortality functions grids" or that there is no communication between "times series" and "fishing mortality functions grids". In my case what I'm going to do is import CSVs with a single simulation, or even 2 simulations if I want to change 2 species at the same time. It could therefore be a bug, but I'll have to try previous versions of ecopath to see if this problem has always occurred. If you have any suggestions, I'd love to hear them! Thank you very much.