I have this routing defined in my module's init.php;
Route::set('store', 'store/<store_id>(/<controller>(/<action>(/<id>)))', 
  array(
    'store_id' => '\d+'
  ))
  ->defaults(array(
    'controller' => 'main',
    'action'     => 'index',
  ));
and the default route in bootstrap.php is still intact.
Route::set('default', '(<controller>(/<action>(/<id>)))')
    ->defaults(array(
        'controller' => 'welcome',
        'action'     => 'index',
    ));
my Controller_Item class;
class Controller_Item extends Controller {
    function action_category($category_id)
    {
        echo 'Category ID: '.$category_id;
    }
}
Using http://mydomain.com/item/category/8
Output:
Category ID: 8Controller_Item and method action_category(8)
The problem is when using modified route;
http://mydomain.com/store/1/item/category/8
Output: 
Category ID: 1