Maybe it's some kind of power-saving feature either on the laptop (prime suspect) or the external drive. I take it the laptop is connected to the wall while it's downloading overnight; if so, disable any power-saving features you might have enabled. Usually you can set up different "profiles" in the power-saving utility.
The HDD might also have some type of power saving features like disk spin-downs. Make sure these are disabled as well.
Also, take a look at this thread:
http://forums.animesuki.com/showthread.php?t=62017