When I'm this close to a deadline I NEVER use ProSeries to withdrawal the payment with efiling the return.  I don't trust the process.   I always use IRS Direct Pay. And Indiana (where I am) doesn't allow direct debit with the return.   Have to use DORpay system. 

So if you can use NYS DOR website to make the payment you desire - do.  At least then you know it was done correctly.