Some users are finding that the tool does not perform, instead offering a message saying that the tool is "unable to optimize your campaign at this time."
Other members say that the Website Optimizer suggests that "www" be appended to URLs.
Finally, others are finding that Google is demanding a lot of money for minimum bids.
I know exactly what you are feeling. Google is insane with their min bids especially for new projects. Some of my keywords min bids jump from: .15 to .02 to .20 to .10 to .30 to .05 to .50 to .04. It is insane.
Forum discussion continues at WebmasterWorld.