For some reason, brother printers (at least mine) do not take into account the settings specified for the printer in the regular way (Gnome settings in my case).
But mysteriously, there is a command which can be used to change them properly (brprintconf_mfc235c). In my case, I was having problems with top margin, and top of pages was not printed. Apparently it was because of page type, so I could fix it by:
sudo brprintconf_mfc235c -pt A4