LDAP users with both manual enrolments in manual courses and LDAP enrolments in LDAP courses are not seeing the manual courses – unless the users have no enrolments in LDAP courses (or in this case, the LDAP courses have been manually deleted). As far as I could tell, it isn't in auth/ldap/auth.php or enrol/ldap/enrol.php, but may have something to do with the LDAP checks done on login.