Do note that there is a difference between module roles and project roles. Could it be that you create those roles as module roles? On the project level you decide the top level roles. And for each of those roles you define which module roles they have.
Thank you for the replies. I have solved this problem. I am not sure how but this is what I did. Firstly I created each entity roles generalization from Administration.Account.
Then in the specific microflow for registering accounts, I assigned each user role to System.UserRole.