On the page with the vertical list of zero values, where you land if you navigate to app engine --> quotas --> view usage history in the dev. console, there is an information label on top saying "These costs are estimates based on App Engine list prices." Estimates may be wrong to some extent, as they are what they are named: only estimates, by contrast to guaranteed and double-checked values. In your case the estimates are all zero, if I look at another project I can see non-zero values. In all cases, these values are provided for orientation and best-effort basis, just to provide an estimate. They are not meant to be compared with the final values (on the second page in your screen captures).
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