USB's far from ideal for hard drives and high speed storage devices. You'll be much better off with sata, esata, or even firewire compared to USB 2.0.
What's the reason you're using usb?
USB's capable of 20-35 MiB/sec ( ver 2.0 ) and it's got latency problems. SATA's capable of 110-155MiB/sec and it could be way more than that.
USB 3.0's been improved but it's still got latency and performance problems, it'll vary based on the chipsets used and how those chipsets are connected to the bus.
Have you looked at System -- Prefs -- Power Management and checked your bios?