it is very well possible that IO is a problem as %util increases significant when running with multiple bshells. Can you describe your disk layout (number, RPM, spread of load, RAID)? How many disks and how fast? When running over 1 hour the cache of a few MB's doesn't help you anymore.
Hope this helps,
BTW: this post has been made on my personal view. My employer might not share my point of view.