If the USB ports are all on the same controller, they share their resources, so the transfer rate with 6 ports would be max 1/6-th of the transfer rate with 1 USB port if we disregard the overhead. Add that overhead to the equation and the transfer rate goes down even further. Now take into account the fact that you are copying from slow 5400 RPM disks that effectively max out at around 80 MB/s with these chunks and high latency, add the OS overhead and these transfer rates do not surprise me.
Also a culprit may be buying inexpensive USB 5400 rpm drives (they could have a cheap USB 3.0 interface) which may also be a bottleneck Not all USB3 devices are equal with transfer rate performance,.but as cc_merchant pointed out you are misusing the USB system. Add another SATA controller card and use the bare external SATA drives.
To add to Bill's comment, let me give you an example that not all USB3 devices are created equal.
ICIDU Slider USB3 sticks manage a transfer rate that is lower than many USB2 sticks. Kingston G4 Traveler are around 10 times faster and SanDisk Extreme sticks are even faster. All are USB3, but ...