Vivian Sinou
I tackled the exact issue last weekend. After loading hundreds of users into the system automatically with the role of "faculty," Sakai replaced their role to "maintain" when it created their sites. Of course, all kinds of things were broken because my 'faculty' didn't have any roles/permissions. The main reason was the fact that I did not have a "maintain" entry under "!site.template.course." I only had faculty, student, guest, and support. I removed 'support' and added 'maintain' in its place and Sakai now is happy.
This is what I discovered... in the process of fixing things:
First, you MUST have a "maintain" entry under "!site.template.course" with the roles you need checked. Or, Sakai will add this role under each course site, anyway, and it won't have all the needed items checked. So, go ahead and created one with all the roles you want it to have. It may be a duplicate of the "instructor."
Now, in addition to the "instructor" role that you add under "!site.template.course," you need to create a realm !user.template.instructor. You can click on "!user.template.maintain," and then click on "save as" to create it.
I was not successful in propagating the changes down to the existing course sites using the !site.helper that's supposed to do that, as per John Leasia, but at least any new sites now have all roles. I had to make the changes manually in the course sites realms.
Hope this helps. I've asked John Leasia to give a session on this in Baltimore. I feel like I understand all this better, but I am sure I have gaps here and there. John may be able to add his two cents here.