FWIW, I thought I had the same problem. But using mainstream kernel
didn't change anything. My real problem is that most of my big files are
downloaded via bittorrent, which ends up fragmenting files *a lot*. See
http://trac.transmissionbt.com/ticket/849 in transmission bug tracker
for example. I used shake (http://vleu.net/shake/) to defragment my
disk, and now everything is fast again. I plan to switch to ext4 to see
if the problem goes away for future downloads.

** Bug watch added: Transmission Trac #849
   http://trac.transmissionbt.com/ticket/849

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Slow SATA performance
https://bugs.launchpad.net/bugs/119730
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