It depends on what you mean by credited - (if you need to clarify, respond to this answer in a comment)
You should be receiving credit for the estimated state taxes paid in January of 2017 for refund / balance due purposes on your 2016 return. The estimated tax payments should offset your current year tax liability. But, you will need to make sure you have entered these estimated tax payments in the program (use the search feature in the top right hand corner of your screen and searching for "estimated tax payments" and click the "jump to" link - state payments go in the Federal section of the program but there is a section for State ES payments).
If you are referring to the itemized deduction you receive on your Federal Schedule A for the estimated state taxes paid in Jan of 2017 - then they go on your 2017 return even though the payments were made for your 2016 return. You can only deduct taxes that are actually paid in the tax year.
So, you will include the payment on next years return. I have included a screenshot of the Estimated Tax section that shows where you would have entered this payment on this years return (it will be the same place next year but different years). But, if you have a payment from Jan 2016 that you need to include, then this is where you would.
