Which USB ports are you using, rear ports from motherboard or front ports from the case. I always use rear ports for hard drives and front case ports for USB jump drives or camera connections.
I use both front and rear. Same problem with any other USB port. Though, other devices work fine. I have a wacom tab, works fine. I have a Logitech wireless keyboard and mouse set, works fine. Powered HDD docks, they worked fine. It's only with self-powered USB external HDD that the problem comes up.