HMVC and controllers

[eluser]MgM Web[/eluser]
Im currently using Modular Extensions - HMVC to implement modules on my site. This is working great until I found out something weird.

Looks like the HMVC takes controll of the default controllers. I am trying to add a new controller in a subfolder "system/application/controllers/subfolder/my_controller.php". But when I try to acces this page using "http://www.mysite.com/subfolder/my_controller" I get an 404 Page nit found error.

But if i create the same file under modules using "system/application/modules/subfolder/controllers/subfolder.php" the page is showing correctly.

Is this the way it is supposed to work? Do I have to create the new controllers inside the modules structure or am I missing something?