Manually deleting the Safari cookies on Yosemite is not working
I don't understand the full interplay, but rebooting will fix cookie retention [presumably held in cache] - that is separate from login details remembered by Keychain &amp; also Form Values etc.

If you really want a clean sweep, try OnyX (free/donationware) > Cleaning > Internet - choose what you need to delete from there…



Safari has its own simpler version, though I'm not certain quite what it does delete…