I can not explain that. Now my server did not like the -h command but likes --host so I ran this command and it works via putty just fine. However yes through the program my database backups are the same as yours.
/usr/bin/mysqldump --opt --host=$host -u$mysql_user -p$mysql_password database table > /var/www/backups/table.sql
This does seem to be related to MYSQL 4 so I will do some searching and see if I come up with anything. This works fine with MYSQL 3