Thank you for the response.
I'm not sure which they are but - most likely cached cookies. Since a quit and restart Safari "apparently" eliminates all those cookies that are not set as favourites in Cookie, it sounds as though that is what is happening. Cookie does delete them but it's not reflected in Safari until it's done a restart. If that is the case then I think Cookie is probably working as intended.
In the past Cookie would show in red those cookies marked as tracking ones. Now it simply lists that there are X number tracking cookies. It would be good if the old behaviour could return.