Thanks, that helped me get in the right direction and I got this solved now.
To explain: For News there is only one menu item directly in the root menu.
Then I've got a movie database with a two layer menu:
- Movies and more -> Movies
- Movies and more -> Actors
- Movies and more -> Directors
- Movies and more -> Publishers
These are the relevant menu items where I had this problem, all off the main menu.
An example for the "correct" link (i.e. the one that doesn't show the modules I don't want) is this: http://www.ratingaction.com/index.php/de/neuigkeiten/filme/from-dusk-till-dawn-neu-in-der-datenbank
As you can see, the link setting is /parent/parent/alias.
So what I did was that I went to the List & Search Type that generates the links, went to the Item tab and clicked on [2] Link + Typography. I then clicked on the + beside the link setting for the field and set the SEF URL setting to SEBLOD (+) -> /parent/parent/alias and set the menu item to the correct menu item matching the content type I'm linking to (in my case "Neuigkeiten").
Now the links are generated correctly and only the modules I want to display are displayed.