I've just had real trouble getting MySQL to start up cleanly. It seems that there is a Linux problem which prevents the MySQL server starting cleanly when a my.cnf exists. See these two mysql tickets:
http://bugs.mysql.com/bug.php?id=29727
http://bugs.mysql.com/bug.php?id=29595
It took me hours to figure out it was simply the *existence* of a my.cnf which was preventing the server start-up.
We're running CentOS but it doesn't seem to be related to a single distro judging by the other MySQL forum reports.
We kind of need to specify some MySQL server config options but I'm not sure how to do it now!
Any ideas?