Maybe try unistalling and then delete the two folders listed below (paths are from XP, but should be similar in Vista) in case there is something being retained during the uninstall which is causing your problems. Then reinstall.
C:\Program Files\Sony\Reader
C:\Documents and Settings\{user name}\Local Settings\Application Data\Sony Corporation\eBook Library
I don't know if it'll do anything, it's just a thought.
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