Question

This makes no sense!
The update query only actually updates if the value is an INT (yes it is defined as text).
The INSERT which has the same variables works with type of value!

mysql_query("UPDATE  `atuam_mae`.`missoes` SET  `mensagemdeuser` =  $message WHERE  `missoes`.`id` =$idmissao;");
mysql_query("INSERT INTO  `atuam_mae`.`concelhos` (`id` ,`tempo` ,`userid` ,`concelho`) VALUES (NULL , CURRENT_TIMESTAMP , $user ,  '$message');");

Answer 1

That is because you are not enclosing your input variable in quotes:

"UPDATE  `atuam_mae`.`missoes`
 SET  `mensagemdeuser` =  '$message'
 WHERE  `missoes`.`id` = '$idmissao';"

NB. Don’t do this and use prepared statements instead!

$stmt = $db->prepare('UPDATE  `atuam_mae`.`missoes`
     SET  `mensagemdeuser` = :message
     WHERE  `missoes`.`id` = :id');
$stmt->execute(array(':message' => $message, ':id' => $idmissao));