Near identical MySQL deployments behaving very different - High CPU Usage problem
This sounds like a configuration issue. INSERT/UPDATE statements result in writes, so you should look at the write path. Check the following:

Is write caching on the disks enabled?
Are the disks configured the same way (RAID geometry, file system, mount options, controller)?
Are your InnoDB transaction logs the same size and configuration (innodb_log_% options)?
Are your disk flushing options configured the same (sync_%, innodb_flush_%)?