MySQL Startup Parameters

Well I just had a major heart attack due to the last mysql server update. It changed my startup parameters that I had in place which changed my sql data directory from the default of /var/lib/mysql to /mysqldata

This is going to sound extremely stupid but I did not write down all the changes when I first worked out how to set it. Currently its set in the /etc/my.cnf
eg : datadir=/mysqldata
which works fine when doing service mysql start|stop however it does not seem to work when i go in via WHM and click restart SQL. Where is this script grabbing its information from to start?

Thanks