Check that the flatrate shipping method has been enabled in the Shipping quote methods settings. That's also the form to set what order the different methods will be displayed.

Don't worry about it. Just trying to give you a hint about what I was talking about.

Back to the problem at hand.
Something like that had been happening on the livetest, but then we updated it to the Bazaar code, and it started working again. Unfortunately, I don't remember what I had changed since the last release that would affect it. If you can get the code from the Bazaar repository, you'll probably fix the problem.