One way to solve this - if you are checking for login - is to create a custom base class that all controllers will use which require an authenticated user. This base class will redirect the user to an authentication controller if they are not authenticated. The authentication controller will not inherit from the base class, which prevents an endless redirection loop.
I have used this scheme to implement authentication in CodeIgniter, and while CI is different than Kohana, they are close enough that it should work for you as well.