The following code fails for the array and is success for the string:

require_once( 'core.php' );

$t_test = config_get( 'main_menu_custom_options' );
print_r( $t_test );
$t_test[0][1] = 20;
config_set( 'main_menu_custom_options', $t_test );
$t_test = config_get( 'main_menu_custom_options' );
print_r( $t_test );

$t_test = config_get( 'default_home_page' );
echo $t_test . "\n";
$t_test .= '?test';
config_set( 'default_home_page', $t_test );
$t_test = config_get( 'default_home_page' );
echo $t_test . "\n";