More than likely, a cron job is running and is executing one of the following:
1) updatedb (to update the database linux keeps of which files are stored on your disk and where they are)
2) daily backup
3) web stats
All of the above will cause large increases in the amount of disk traffic. You can imagine your server's HD rattling and chugging away. This causes other processes to have a hard time communicating with the disk and therefore more and more processes build up and get in line. Next time the load goes up, try looking at the processlist to see what is happening.
will show you most of the common programs that would cause a high iowait on a typical webhosting box w/ cpanel or ensim for example. You will have to either grin and bear the high load or remove them from the cron if they don't serve a purpose.
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give it about an hour to kick in should help loads. If it does add them to /etc/rc.local
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