i doubt very much IRS is going to correct your return if your 5329 shows a penalty but that is because of a miscalculation by tax software.
Another solution not mentioned is to file with a penalty but request a waiver of the penalty.
A waiver request must be supported by a "reasonable" explanation.
Is it reasonable to explain that your return calls for a penalty but the software doesn't work right?
Perhaps you would have to explain further.
When you request a waiver, you don't pay the penalty up front.
@dan_in_MI
