http://dev.mysql.com/doc/refman/5.0/en/invoking-programs.html

<quote>
The default hostname is localhost. For client programs on Unix, the hostname 
localhost is special. It causes the client to connect to the MySQL server 
through a Unix socket file. This occurs even if a --port or -P option is given 
to specify a port number. To ensure that the client makes a TCP/IP connection 
to the local server, use --host or -h to specify a hostname value of 127.0.0.1, 
or the IP address or name of the local server. You can also specify the 
connection protocol explicitly, even for localhost, by using the --protocol=tcp 
option.
</quote>

so this is a feature of mysql
setting this bug as invalid

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MySQL Query Browser ignores port number
https://bugs.launchpad.net/bugs/155466
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