Comment 5 for bug 1454917

I found the source of the problem -- the RPM script is not following the rule that when multiple instances of a given option are found, the last instance takes precedence. A similar issue caused bug 1201036.

Excerpt from the documentation
http://dev.mysql.com/doc/refman/5.6/en/option-files.html

If multiple instances of a given option are found, the last instance takes precedence.

My /etc/my.cnf file ends with an include directive

<!includedir /etc/mysql/conf.d/>

and the /etc/mysql/conf.d/001-basic-config.cnf file contains a duplicate pid entry

# tail -1 /etc/my.cnf
!includedir /etc/mysql/conf.d/

# grep -i pid /etc/my.cnf /etc/mysql/conf.d/001-basic-config.cnf
/etc/my.cnf:pid-file = /opt/mysql/dbprod/monty-q0.pid
/etc/mysql/conf.d/001-basic-config.cnf:pid-file = /opt/mysql/dbprod/monty-q0.pid