If Box 1 and Box 16 are the same, then the adjustment that is being made when the entry is made in Box 14 appears to be correct - it's adding the pre-tax (federal) deduction back to the NY income (where it's not deductible.)
The difference between Box 1 and 3 is where we see that contribution (and likely other things) deducted from your federal income, as the deduction doesn't "count" for social security tax purposes.
For the scrubbed file - does your program have an "Online" menu instead? Send tax file to agent is located there in desktop versions of the program.
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