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@TaxLaw wrote:

same issue all monies paid 6 weeks prior filing date. How to remove remove IRS penalty from program prior to electronic filing?

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As was mentioned above, if ProSeries is calculating a penalty, most likely you are looking at the Estimated Tax Penalty.  That DOES often applies even if payments were made by April 15. (the Estimated Tax Payments were due to to paid during the prior year on April 15th, June 15th, September 15th and January 15th).