Tableau uses an accent-insensitive comparison for geocoding names, so Habo = Håbo. The best fix would be to include the län in your custom geocoding data since the two kommuner are in different län.
The other option would be to rename them in your custom geocoding data so that Tableau could see them as different. For instance, name them Habo, Jönköping and Håbo, Uppsala.
I'll think about how we might make this better for you in the future.