I recently helped a colleague with a MySQL database administration issue he was dealing with which had him stumped for some time.
He was trying to modify the connection timeout limit for the database server. The default was 28800 seconds which was far too long for their use. After a quick look at the MySQL documents he read the sever setting to adjust this was wait_timeout and interactive_timeout.
Now after setting this in the my.cnf and restarting the server there was no change in this setting. He tried a number of other things before asking for help with this annoying problem. After a quick look at the my.cnf I could see he added the two new settings at the bottom of the my.cnf file which was causing the issue.
my.cnf is separated into sections using brackets to define each section like [mysqld], [client]and [mysqladmin]. Where the new setting had been added to the bottom of the my.cnf file it was actually in the [isamchk] section. After moving it into the [mysqld] section and restarting the server the new setting had taken affect.