Public bug reported:

Binary package hint: mysql-client-5.0

>From mysql --help:
Default options are read from the following files in the given order:
/etc/mysql/my.cnf ~/.my.cnf /etc/mysql/my.cnf 

Because /etc/mysql/my.cnf is checked twice and ~/.my.cnf is not the
final check, customizations in the local settings file that are
duplicated in the main settings file (such as the port option) are
overridden.

** Affects: mysql-dfsg-5.0 (Ubuntu)
     Importance: Undecided
         Status: New

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MySQL client improperly checks settings files
https://bugs.launchpad.net/bugs/159563
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