The way vBulletin usually works is, if you have groups A and B (not your scenario!) and B has all permissions but A can only view, then this would be the scenario
Primary A = Can only see stuff
Primary B = Can do everything
Primary A, Secondary B = Can do everything
Primary B, Secondary A = Can do everything
It works like this because higher permissions always win, the only thing you have to do is check the forum permissions for those usergroups, if my usergroup B (who can do everything) visit my sub forum "x" and i have set permissions for that forum for that usergroup to only see stuff then my settings win and their permissions do not.
Does that make sense?, so maybe your permissions for the usergroup are correct but the permissions per forum per usergroup are not