The type of motherboard that you are using, along with the controller on the motherboard that you are connected to and drivers all can have an affect on the hard drive performance. On an Intel H77 chipset motherboard is is recommended to have the hard drive connected to a SATA port controlled directly by the Intel SATA RAID controller. Some motherboards have additional onboard controllers from other vendors to give additional SATA ports. File transfer speed is going to depend largely on the types of files that you are copying. To get the best judge of performance transfer a single very large (multi gigabyte size) instead of many small files.
When you are transferring files are you moving them from one location to another on the same hard drive, or from one physical hard drive connected by SATA to another physical hard drive connected by SATA? USB 3.0 should allow plenty of throughput to allow the drive to transfer at it's maximum throughput depending again on the hard drive, controller, drivers, etc.