Exactly the same happens here with Transmission, qBittorrent and Deluge (Ubuntu 11.10 32 bits with all updates, hardware Lenovo Thinkpad X200). A old dicussion of this (Karmic) can be seen at https://bugs.launchpad.net/ubuntu/+source/ecryptfs-utils/+bug/431975. My workaround: create a folder /home/BT (non encrypted), adjust permissions and download torrents to it.
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