Hi Gary,
Good to know it's working fine =). Your settings seem ok. You can check to see if your students have student roles assigned at course category level (very unlikely) if this happens again. You can find any student who can access the entire site, find his/her userid (just go to his/her profile page), and check what assignment he/she has in the role_assignment table.
Cheers,
Yu
Roles and permissions
Students enrolled in all course - the saga continues!
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