It is a MAS version.  I copied the .plist files to a temp dir, killed the process with activity monitor, deleted the app at both the user and system levels and re-downloaded from MAS.  Then brought back the .plist files and all is well.

With version 5, does Safari no longer show cookies deleted by Cookie5 while Safari is still running?  If so, I will upgrade to it.

When I click on Cookie in the Menu Bar, it shows the usual menu choices, but everything is grayed out except help.

I am running El Capitan with the latest updates and Cookie 4.5.5

This is still happening. It runs for a while, then quits deleting after X minutes. Mine is set to 5 mins.
I can get it to work again by deleting the cookie .plist file.

Please look into this because it is basically making Cookie no longer useful. It is a wonderful app, when it is working right. I need it to work because I never close Safari. I am running on Mavericks.

Mountain Lion 10.8.4
Will Cookie continue to work on Mavericks?

Looks like there may still be a problem. It works intermittently. 3.0.18 version, Macbook Pro, Mountain Lion, Safari (everything up-to-date). See these screenshots taken while I was on a single web page for 30 minutes.
They show a 5 min delete period and 247 cookies. 12 are Favorites.

With more testing, it was version 3.0.17 that was broken. 3.0.16 and the latest 3.0.18 work. Sorry for not updating before commenting on a bug.

This is the same problem on Safari running on Mountain Lion. It used to work.