Module options missing when using multi-tenant

new install running Version 12.6.0

when using the primary site created at install all works as it should, however when i go to a site created after i get limited options. its all there just not available form the menu options. i have attached screen shots to show you what im having issues with.

I have all permissions enabled and even tired 3 different browsers to make sure it was not a fire fox issue.

user on the new site have permissions to those missing modules/doctypes? seems like a permission issue