In Box 12, it is subtracted from your federal income, but not always from state. Are Box 1 and Box 16 different? If so by an amount similar to the pre-tax contribution? (There can be other things in that difference, so it may not be exact).
If Box 16 is less than Box 1 by the contribution amount (or roughly), then it's likely it's just adding it back for NY purposes - which is what I would expect it to do.
If you don't mind, you can send me a "scrubbed" version of the data in your return (replaces all personal info with placeholders) by going to Tools, then Tax Tools, and selecting "Send File to Agent" in the pop up box.
That will give you a six digit code that is safe to post here and will allow me to see the numbers to see if I can make any sense of them.
If it's taxing you twice this way, then I think the return will have to go by mail. If it's only adding back to the NY taxable income the amount then it's not - but that only works out right if the Box 16 number was adjusted (which is typically how it works, but there are always situations that aren't typical.)
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