Manual scaling specifies the number of instances that continuously run regardless of the load level. This allows tasks such as complex initializations and applications that rely on the state of the memory over time. If you choose manual scaling, and, as a consequence, your instance runs continuously, you will be charged for the amount of time the instance runs, that is, in this case, all the time, as documented on the "App Engine Pricing"
page.
By contrast, you may have no instance running when you have chosen automatic scaling, so no related costs. As mentioned on the same page, basic or automatic scaling: accrual ends fifteen minutes after an instance finishes processing its last request.