This is a fix of Top Level Categories plugin for WordPress 3.1. and above.
We recommend that you use the Redirection plugin and add your old an new category links, or use a Regex redirection rule. Make sure you change Tools -> Redirection -> Options -> URL Monitoring to "Don't monitor", as there is a bug in that feature (also in latest current version 2.2.5) - not related to FV Top Level Categories.
Make sure your categories have unique slugs - watch out for pages with the same slugs. Normally WordPress uses the category prefix to distinguish page from a category, but with this plugin you need to make sure the slugs are unique, otherwise some pages might turn up instead of categories.