I have heard of a few people getting the same problem with Spybot's automation.
To find any remaining registry keys run regedit, (click on 'Start', select 'Run' and type 'regedit')
Choose 'Edit' from the menu and then 'Find' and search for spybot.
You can then delete any files found.
Important: I would only recommend editing the registry if you know what you are doing as you could cause serious damage!