If you try to start MySQL server using the preference pane it fails. I tried to start it using '/usr/local/mysql/bin/mysqld start' and it still failed.
Here is the fix for the preference pane start and stop.
Edit '/usr/local/mysql/support-files/mysql.server'
Find line 'basedir=.' and replace it with 'basedir=/usr/local/mysql'
Here is the screenshot after the change:
After this, I was able to successfully execute the following commands:
sudo /usr/local/mysql/support-files/mysql.server start|stop
SystemPreferences > PreferencePane > MySQL Start|Stop Server
This fix came from: http://bugs.mysql.com/bug.php?id=53232
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