You have an interesting question. With the information provided, i can make an "educated" guess. In my experience, Turbo Tax requests information about the year-end values of IRAs taken from Form 5498. The information is entered in the Turbo Tax input area for determining how much of previously nondeductible contributions can be recovered as non-taxable income from the previous year. You should be keeping a record of your previous nondeductible contributions and how much of those nondeductible contributions have been recovered in previous years tax returns. Turbo Tax is performing that chore for me, and no doubt is for you, if you are a continuing customer of theirs.
With the forgoing in mind, it seems to me you should be seeing your refund increased, not decreased. So, I suggest you don a thorough check of your input to make sure you are entering your information correctly. It may be helpful for you to look at the 2016 Form 8606, if one is included in your 2016 federal income tax return.