@LukeMN It is still possible to have an underpayment penalty: if you don't pay the estimated payments on time. And you are correct that all of this can be affected by alternative methods of calculating the amount of payment that needed to be made by the quarterly payment deadline. But double-check everything, including your entries, to make sure your inputs are correct, and then, if they are, you may wish to contact customer service to resolve the processing issue you are experiencing. The following link has more information: How do I contact TurboTax?
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