Thanks for the followup.
The App Store wasn't letting me re-install Cookie, having deleted it, because I had a back-up drive mounted, and the Store was reading Cookie installed on that drive.

I'm running 10.10.1, Safari's unchecked in iCloud, and I have run the command line. Safari history is never deleted by the timer but only when I quit the browser. Cookies have the same problem. Any thoughts?

Also, how do completely uninstall the application that was purchased via the app store? Ive tried deleting it to reinstall, but the App Store says it's still installed.