The problem shown should not have anything to do with the partitionsing, a drive should be able to keep up (generally) with the USB2 speeds, even at the slower end of the drive.
Those speeds look terrible, but does not really say much, because file size can make huge difference. You also did not indicate the location of C:, C is primary internal ? is this on a desktop or laptop?
Viewing into a directory that is changing, can slow things down some (simultaneous I/O). By not looking:-) the system wont be doing "other things" at the same time in that folder location. On the Other hand :-) if something is going on besides the copy, seeing hidden files might be useful.
The speed is faster than a re-negotiation to USB1 type speeds, so it is not likly that a cable or interferance or some minor power issue is setting the serial transfer speed lower, But it could be some sort of connection problem?
Some test might be usefull. I use a simple and quickee tester called "CliBench" , as opposed to more extravagant testing for quick looks. I would check the speed of both drives.
If the speed of the drives (either) is very badly low, and the systems tool do not show a lot of other stuff going in (which there always is), then doing a SMART check on the drive might be in order, to see if there is odd numbers of seek error or something?
A person could try Terracopy and or FastCopy , these use large non-system ram buffers for copying, and tell the speed, Where are you getting the speed info from now? What is the method used for copying?
Is there anything odd showing up in the resouce monitor, or the task manager? Odd use of memory? Switch BOTH of these tools so the columns show "bytes read", and "bytes write" and look around. Virus prevention software, or other 3rd party software might be scanning the files, viewing the I/O in these tools, should help to identify that. A virus scanning software might be stopped temporarily from an Active scan, to complete a file operation.
Is the (finnaly) transferred data 100% bit for bit Perfectly the same? A comparitor or using Copy methods (above) that do full compare of the data, could identify if there is a corruption transfer problem, via Motherboard ram, or somewhere along the line.