This happened to us using GCO mod 1.4.1beta1 in ZC 1.3.7. We were accidentally offering $1 shipping for FedEx First Overnight! (ouch!)
The fix in this version is to edit the googlecheckout/shipping_methods.php file and comment out (or delete) the entries for the individual methods you do not wish to use in each of the shipping-module-related arrays of methods. This is specific to Google Checkout; deactivate methods you don't want available for Google Checkout, even if you are using them in ZC checkout.
Then go to the admin UI and set reasonable flat-rate defaults for any methods you are using. These are used whenever Google Checkout cannot communicate with the shipping module to get a live calculation.
The setup may vary a bit in later versions of the mod. In those versions, you may be able to do it all in the admin UI. But in 1.4.1beta1, you have to edit the shipping_methods.php.
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