Copying files is not generally a good way to determine throughput due to OS & protocol limitations. I assume these are 3560G's with hosts connected at 1Gbps and not standard 10/100 3560's......
I would make a baseline using just a cable between the two hosts and perform the file transfer to see what speed you achieve. Once you have this you should perform your testing again and compare the results. If it is wildly different then it's possible you are having a problem.
There are known issues if you have QoS enabled (CSCsc96037) so that could be what you are hitting, however I would still perform the baseline as I suggest and go from there.
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