Using CCleaner to wipe browsing history on Chrome, it will wipe the history so you can't see it through the browser, but if I go to C:\Users\%Username%\Appdata\Local\Google\Chrome\Userdata\Default I can open the History file and the Cookies file with notepad and all the history is still there.
Can you confirm if the list of sites saved in the history is in fact a selection of websites that you have bookmarked? And is the list of cookies ones that you have listed to save in Options > Cookies?