Switching to Debian 7 and percona-mysql-5.5.16 amd64 from percona repository started experiencing unusual slaves slowdowns. After some research, I found that there are some strange locks happening during "drop table" (already emptied). While not discussing why drop empty table on server with big (50Gb) innodb buffer pool slowing down servers drastically, I created a workaround adding "engine=myisam" to /usr/local/bin/apply_diff_relay_logs line 370:

"$_mysql --user=$_escaped_slave_user --password=$_escaped_slave_pass --host=$opt{slave_ip} --port=$opt{slave_port} -e \"set sql_log_bin=0; create table if not exists mysql.apply_diff_relay_logs_test(id int) engine=myisam; insert into mysql.apply_diff_relay_logs_test values(1); update mysql.apply_diff_relay_logs_test set id=id+1 where id=1; delete from mysql.apply_diff_relay_logs_test; drop table mysql.apply_diff_relay_logs_test;\""

After that, problem has gone as expected. Probably this change could be useful in main code.

Debian 7.6, linux 3.2.58, mha-node 0.56, percona-mysql-5.5.16 x64