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bbfa235
(Get the code!)
Peter,
I wish I had a more helpful answer to give you, but all of this sounds consistent with my previous comments --
(1) Linux's NTFS drivers do not play nicely with high volumes of random disk reads and writes, such as those generated by p2p applications. You may want to use a different filesystem than NTFS. (The same holds true for encrypted filesystems, by the way.)
(2) You can also try to reduce the frequency of disk reads and writes by using Transmission 2.10 or higher, which has a memory cache for this purpose. I know about the ppa URL listed above, but I'm not an Ubuntu user myself, so I don't know how to use that URL in Ubuntu. Your Linux Expert friend might have better ideas on this.
(3) If the hard drive is literally buzzing from the strain of all the disk reads and writes, it also may be a sign of impending disk failure. You might want to make a backup of that disk before doing anything else.