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I think at the time you posted it was pretty much peak hour. I can also explain the improved performance before the scrub:

We also switched back to deadline io scheduler, since the upgrade to 12.04 we were stuck on cfq which impacted things greatly.

I've adjusted read ahead values on the underlaying disks on the raid during the scrub so it would finish faster, I don't know if it has a impact on day to day currently.