The full distribution is used when starting a new site. It has default flexwiki.config and web.config files

The update distribution is used to update an existing FlexWiki site. It has no flexwiki.config file or web.config file, so that settings in those files are retained during update process. It does have a favicon.ico file, which may need to be deleted from the update distribution prior to update if you have a custom one already in your site