Multiple tool selections displayed twice with useToolGroups enabled

If tools which can be selected more than once (e.g. Web Content, News) are selected for a site, they appear twice, under two categories, when config.sitemanage.useToolGroups is enabled (SAK-16600).

The tool will appear once under the category it's defined (but without identifying info), and again under the Ungrouped category (but with identifying info). See attached screenshot.