"Show Your Top Sites" is the most frequented items in your internet history when you open a new tab.
If you start a new tab and "Show Your Top Sites" is checked the thumbnails disappear after being Cleaned but the URL's still appear under each blank thumbnail.
Internet history including cookies is checked and does get cleaned but not for "Show Your Top Sites" history.
Windows 7, Firefox 50.1.0, CCleaner 5.25.5902
thx