Some of the J2EE roles you created under Studio->Manage->Studio->Roles may not be visible after the upgrade. Those roles are all still available but do not display because some new information Enterprise Portal 6.0 expects on roles is missing.
To correct this, log in to Portal Studio and create a new portlet of any kind. During the Save operation you will see the Properties sheet and on that sheet will be listed all “Available Roles”. Use the Add All button to assign all roles to this portlet, and proceed with the save. Once these roles are referenced, the additional necessary information is automatically created for these roles.The next time you go to Manage->Studio->Roles, those old roles will display correctly.