I would recommend that you take a look at the access.log and see what path is generating a 404. Then go take a look at the user in question and see if you can see which group is causing a restriction to that path.
One of the things that the LDAP connector will do is automatically add groups to users - its possible if the LDAP connector is adding a new group to your LDAP users that group might have deny permissions on it that are overriding the standard group permissions.
Even if that's not it the LDAP connector itself is unlikely to causing this, either permissions of the existing groups have been changed some how, or the LDAP connector is adding groups to the users and those groups are overriding the standard groups. So I would look at the users in question and verify that their group assignments are unchanged and that they still have all the right groups and don't have any new groups.