I'm experiencing the same problems and had no idea before reading this
that they were related (I recently replaced my hard drive and just
started using an encrypted home directory). Specifically:

1) Pre-allocating space takes longer than "normal";

2) I am seeing a really high percentage of corrupt chunks. Only recently
have I started having Ktorrent rescan torrents after they've completed
downloading (after I noticed a few were corrupted). Now almost every
file that completes has a large number of corrupt chunks, so the
torrents have to be re-downloaded several times before I get a good
copy.

3) I started experiencing the lock-ups over the past few days and have
been banging my head on the desk trying to figure out where the problem
is. I haven't been able to spot anything that stands out in the logs and
can't think of any updates that may have caused the problems.

-- 
KTorrent hangs whole system when rescaning data
https://bugs.launchpad.net/bugs/482509
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Bugs, which is subscribed to ktorrent in ubuntu.

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