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my.cnf: http://pastie.org/9375234
processlist of Percona Server 5.6: http://pastie.org/pastes/9375240/text
zabbix_server.conf: http://pastie.org/9375266

It should also be noted that when Zabbix server is running, Percona Server experiences an extremely high disk load, which makes the rest of the server extremely slow with default options (except the larger cache as detailed in the environment). Here's iotop when the queries are sitting at "Creating sort index": http://pastie.org/9375243