That's the point. Appengine is changing their pricing from CPU hours to Instance hours, so an app that previously had 3-4 hours a day is now going to have 48-72.
Damn it. It appears the only solution is limiting the amount of instances in the application settings. I manage a free sync service with approximately 20,000 active users on App Engine. I just checked the billing history for our application and saw similar results, the cost will increase 10 fold.