I just noticed this during the past week.  I haven't a clue why it happened or how to fix it after searching the support forum.

Cookie 5.9.1
OS 10.12.6

P.S.  I have no thread subscription options in Safari 12.0.

Still dealing with the favorite cookie problem and something happened today that may be a clue about what's happening. . .

I checked my 5 favorited website cookies and there were 0 cookies saved. So I unchecked all of them and deleted the five domains. Suddenly 25 different website cookie sets appeared in the Cookie Safari window. However, Safari listed only one saved domain (I mainly use Safari).
I made a screenshot of the Cookie window with the 25 domain cookies.

Russell, why would I highlight red cookies? Aren't they tracking cookies? Those are the cookies that are trashed when I click "Remove all tracking cookies."

One service for which I want to retain my login cookies is "Our Groceries", an iOS shopping list app. It also allows list management via its website. The two cookies it sets are not red in Cookie.

I've recently noticed that my login cookies are no longer working.  I save them as favorites and click the "Remember Me" button on my favorite websites. But I still need to manually login when I visit a website after I reboot my Mac.

to be honest, im not sure you can even purchase it on the Mac App Store if you don't have El Capitan running on your computer?

I just tried and it won't download.

Your email announcing Cookie 5 and other places I've looked do not note that your license terms are the same for App Store and SweetP Production store purchases. You should consider adding that info in the future.

I did a search of this forum to find out that the license terms are the same. I'll just buy it direct from you.

I am running OS 10.10.5 and I do not plan to upgrade to El Capitan soon.

If I order Cookie 5 and download it will it automatically replace Cookie 4? Or can the two apps live in harmony in my Applications Folder until I upgrade?