If you are copying from the (physical) OS disk to the external, you have to consider all the interference you may get form the accesses the OS makes. That keeps pulling the arm away all the time from your copy job. In such a setup, no two copy jobs will be the same.
This may be the answer to the problem...at least I understand what you said, but if it is the case, I guess that I will just have to learn to live with it, because I doubt that much would help. At least, I assume that by OS accesses you are speaking of something that is beyond operator control.
Have a look into Resource Monitor > Disk tab. The graphs on the right side give you a pretty good idea on what your disk(s) are up to.
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