When you have one default smtp server configuration at koha_conf.xml (we called 'A' ) and another smtp server (we called 'B') at administration UI with two libraries that one of them is set it to default and the other set it to the smtp server 'B' then when the process_message_queue.pl is executing in order to send notices, users from library with the default server not receiving anything , but the users from library with the 'B' smtp server receive everything. The configurations between the two smtp servers A and B are the same, just one time we have passed as default on xml and the other as smtp server from UI , it seems that from UI the functions etc is working better that to get values for the object from xml.