Start preferences shortcut in RTW folder or in Menu Start/Europa Barbarorum.
Have you done this?
EB 1.1 comes with application that lets you to change common options (banners, minimal ui, unlimited men on battlefield, green arrows) withought messing with txt file. And this is what I was referring to.

How do I do that? Do I just erase the "fasle" or "true" and type the opposite in?
But if you insist on messing with txt files it should work as you have described it.