Since you are unable to replicate the issue on your own system, it seems that it is a behavior happening only on your customer system.
So I would suggest performing more tested on your customer system, like running with less memory RAM, or making sure no RAID configurations are available.
Check if the processor on your system is the same model of the one on your customer system, since different processor might have different behaviors or results.
I am having the same issue on 3 different servers where we're looping 20,40,60 times on a compression of an image file. all three servers have sandy bridge xeon processors, same generation as OP. We get inconsistent readings, going from 40ms (optimal) to 80ms spikes throughout the test. 2 of these are running on physical hardware and one is on virtual machine.
These same test ran on older generation Xeons and i7 processors doesn't run into this issue, consistently getting the fastest time through the whole test. One thing I did notice is the Sandy Bridge processors are stuck at 1100mhz, and rarely shoot up to it's max frequency. I have tried booting with turbo boost, c1e and c-state off, and it does not force the CPU to run at max frequency. There is a serious performance hit with these processors and i can't figure out why. On an older server with a xeon x5000 series with c1e, turbo boost and c-state on, it stays running at 3.5ghz and ran the tests flawlessly.