NYS 2016 Amended Return Problem

A dividend was reclassified as return of capital. My NY tax goes down $35. I have done all the paperwork and am ready to efile. The problem is, the IT201X ignores the $326 penalty I paid, and wants to refund me $361.

IT201X LN62 5027 Correct (New tax, less penalty) LN79 5388 Correct (Old tax, plus penalty, amount paid) LN80 361 Wrong (Tax difference, ignores penalty)

IT2105.9 LN24 326 Correct (Penalty paid)

I suppose if someone there (or a machine?!) subtracts IT2105.9 LN24 from IT201X LN80 all will be well. But it looks to me that the penalty should appear on IT201X somewhere, but doesn't.

Am I making an error somewhere, or should I just go ahead and file?

I am tempted to just eat the $35 rather than risk an error. I had a very similar problem on my 2017, only I owed them $64. The stupid software said I owed $0, and I filed before I noticed that. They sent me a bill for $64. If they caught that, they ought to get this right. Right?!

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