The problem with USB is that it uses a master/slave architecture which relays on the main processor to do much of the work. Depending on what is running at the time, available memory, and OS configuration, you may never see the theoretical speeds USB-II claims. Firewire uses a peer to peer protocol where the smarts are in the peripherals themselves. THis allows for much higher throughputs especially in sustained data transfers.
Secondly, your hard drive may also be a throttle. You may be able to get the data to the PC very quickly but it fills up the hard drive buffer and your waiting the the hard drive to write all the data. There are lots of things that can affect hard drive performance such as a single drive, lots of paging, other applications using the drive as well, a slow drive or a small buffer.