I'm using R-Wipe&Clean 11.6 Build 2145 on Windows 10 Pro x64 1607, along with Chrome 55.0. I've found that RW&C deletes all Chrome cookies, even those I have moved to the "Favorites" area. This occurs when I have a task set up to clear Chrome data on "Every Closing a Browser", with of course "Google Chrome" selected. The "Cookies" item in the TreeView pane for this task does show a half-selected status, meaning that some cookies have been favorited.
I am using multiple Chrome profiles, but I am not sure if that is related to the issue. What happens is that RW&C deletes all cookies from all profiles, or it will seemingly randomly leave cookies for just one favorited site, and delete all other cookies, favorited or not.
I am sure that the cookies are not being deleted by any other software, nor by Chrome itself. For now, I have cookie deletion disabled in RW&C, and I only have this issue when it is enabled.