[Hampshire] Slow computer

While moving data around, my computer becomes very slow. Is this to be
expected?

Specifically: when moving tens of GB of data between harddisks the
computer would get slower and slower, and eventually be unresponsive
after a few minutes, until the the move had finished. Also the
application I have on the Gnome panel for monitoring stuff would show
the load average increase to about 20. However, examining the output of
top would show no more than about 8 processes using the CPU at any one
time and that, except for one, they'd never use more than 50% CPU
combined. That one is a background process that I run at lowest
priority, and it would still be quite happily using 100% CPU. (I have
quad core so, given previous examinations of top, I presume I could in
theory have 4 processes each running at 100%.)

So, in summary, I am confused by the fact that a low priority process
can happily continue to run, while the user interface grinds to a halt.
Is this evidence of an underlying problem, a mis-configuration, or a
lack of understanding on my behalf?

Leo

PS The computer is a (quad-core) Pentium Q6600 running at 2.4GHz with
4GB RAM using Ubuntu 9.04 amd64. The harddisks are all SATA.