In case I wasn't clear, I wasn't confused as to why it was there. Apple certainly doesn't make dealing with cookies easy. But I was wondering why it never goes away. Once it is triggered it stays in the menu bar, spinning away, until I make it stop. Even though it says it's 100% done.
It's very possible that this is a problem with just me. And any Automator script would cause the exact same thing. I'm not concerned about it, I just wanted to mention it in case you received some other reports saying the same thing.
Thanks for Cookie by the way, it gives me a little peace of mind.