The script /auth/ldap/cli/sync_users.php doesn't syncronize user custom fields. It return the following warning
Notice: Undefined property: stdClass::$profile_field_mycustomfield in <absolute path to my install>\auth\ldap\auth.php on line 1022

The method user_update_user called by the ldap plugin doesn't save the custom fields.

If an user logs into moodle, the login procedure calls authenticate_user_login(). That metod calls the ldap plugin but ends with the call of profile_save_data() that saves the correct informations.