Over in the Assignments forum, a new Moodler using 1.9.9+ is having odd permissions problems. Permissions for Assignment are missing at the site level in every role! In addition, non-site-level roles (e.g. a student enrolled in only 1 course) list all courses on the site as their courses on their profile.
Since this is beyond my knowledge, I thought I'd add a pointer here to the discussion http://moodle.org/mod/forum/discuss.php?d=160555#p704320