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Why was the payment that was submitted through the bill-pay system sent back?
Whether or not the case will be dismissed is up to the trustee. If you can convince him that you do have the money, and you did not know that paying with a bill-pay system was not allowed, there is a good possibility the case will not be dismissed.
However, to convince him that you do have the money, you should get the money to him as soon as possible (perhaps you can bring it to his office). And it will definitely help if you include the January payment.