I had some problems with my fingerprint reader for quite some time, probably since upgrading to Jaunty. It took multiple attempts to read my fingerprint, and often it wouldn’t succeed at all. So I had stopped using it.
Today, while I was researching a different problem I found a solution: upgrading the Thinkfinger libraries from ppa helped. I added
deb http://ppa.launchpad.net/jon-oberheide/ubuntu jaunty main
to my /etc/apt/sources.list file and updated the Thinkfinger libraries, and it started working again!