It happened to me too. Using transmission as torrent downloader. 
My file system is approx. 7 GB. I was downloading a torrent that had a file 
large 13 GB, of course that file was unchecked. transmission probably failed at 
reorganizing parts and added that part I didn't need. I am running Ubuntu 
10.04, latest kernel and I doubt it's related to the graphic drivers.
So I went to analyze the data used, and /home/me/.Private was 3 GB.

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KTorrent hangs whole system when rescaning data
https://bugs.launchpad.net/bugs/482509
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