Menu API not switching menus?

_Menus are somewhat confusing around there. Try this:

$args = array(
        'theme_location' => 'main-navigation',
        'container_id' => 'navigation',
        'fallback_cb' => 'wp_page_menu'
        );
    wp_nav_menu($args);

theme_location tries to display menu that is attached to this location. menu tries to display menu by slug/id (not location of menu, but actual menu that you create in admin area).

So you are mixing up location with menu slug, it gets confused and just serves first menu it can.

See wp_nav_menu() documentation for full description of logic behind it.