You need to create a top level category within Kunena, which will hold all your GJ forums. Once done navigate to GJ > Config > Integrations > Forum and ensure you select that top level category. Now just create a category followed by a group and it'll auto generate the forums. To fix for existing groups simply run tools and it'll provide a fix link.

Do not touch permissions. Create your top level category. Configure GJ to use that top level category. Now create categories/groups within GJ. That's all you need to do and it'll handle the creation process and set permissions to what is necessary. If you've manually created the forums then delete all the sub-categories of your top level category in Kunena and run GJ Tools and it'll have a Recreate All link. Forum access is based off Group access, do not adjust it to anything otherwise or it probably won't work.