All manual settings get wiped out when saved in My.cnf, why? When I open my.cnf to enter manual setting like:  

innodb_buffer_pool_size = 50M
innodb_log_file_size = 15M
bulk_insert_buffer_size=25M
log-slow-queries = mysql-inja-slow.log


All of my settings get vanished when I hit Save! My server has mysql  5.1.
I solved the problem with :  

chattr -i /etc/xxxx/x/x/my.cnf