When this is happening open Activity Monitor and look in the CPU tab and sort by CPU% and see what is up top using CPU cycles. I'm betting you will see the process mdworker going nuts there. mdworker is the process that indexes your drives for the Spotlight index.
What is happening is even though you are only downloading one file, the way bit torrent works is it is actually downloading hundreds and hundreds of small pieces of the actual file and placing them on the external drive you selected. This triggers the Spotlight process to index those files and it goes completely bonkers.
If you insist on downloading directly to the external drive you can prevent Spotlight from indexing that drive by adding that drive to the privacy pane in Spotlight preferences.
