Roles and permissions

So, we just upgraded to 1.9 and have been figuring out the whole quiz context and category system. And of all things, it's affecting the teacher/professor My Courses Block.

Here is what happened:

1. I needed to move a professor's quizzes into his department (counseling) course category so that he can edit his current quizzes

2. I then had to assign him to that category. So he is now a part of the counseling course category. He is the first member whom I've added.

3. As a result of him being part of that category, his my courses block when from just showing his current courses to showing ALL of the courses in the counseling department.

This means a lot of sifting and searching for the professor to find his current courses.

What I want to do:

I want to keep him in the counseling course category, and for ONLY his courses which he is teaching to appear in his My Courses block. I can't find anything in permissions/define roles to fix it.

Any help would be greatly appreciated,

Aaron