Mysql root password change by some one

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http://serverfault.com – I'm confused, I have a server that is accessible to the public, but I've been 3 times I was in the locker mysql root password by someone else, who knows the password that's just me. I've checked on the local web I do not find php injection and the like, and I already turn off the function exec in php like pasthru, exec, shell_exec, etc. I'm using Ubuntu 10.04 Server. MySql Ver 14:14 Distrib 5.5.17. Webserver Nginx. PHPserver php5-fpm. My question is: Is there an app that can change mysql root password, or that work to others, if it's someone else about where he came through?. Thanks. (HowTos)