I already corrected this in the editor for nearly all the German clubs. Even though there are still teams from Bavaria or North Rhine Westfalia, that are playing in Schleswig-Holstein league at the beginning of the 2nd season.
Furthermore, I added a number of teams from Schleswig-Holstein and put them into the "German Lower Division" so that they can promote to Schleswig-Holstein league but none of them actually promotes. There are 10 - 12 teams from North Rhine Westfalia that promote to Oberliga but none from Schleswig-Holstein.
If you're sure you've done everything correctly yourself, then I'm afraid it's a problem in the game itself.