Not sure anyone could help without more information ... so I'll ask some questions ... but may not be the one who responds further ... depending upon your responses:
Specs of server ... memory is? Is it using swap space? is it remotely hosted? Virtualized?
What is operating system?
Version of MySQL? Do you have anything on the server to check the config of MySQL ... like mysqltuner.pl?
With the questions above, Is production site same as your clone?
'spirit of sharing', Ken
