"why does this result in the original $2,000 / each being TAXABLE Roth conversions?"
It doesn't. Make sure that when you enter the total of $6,500 each as your contributions for 2016 you also indicate that $4,500 of that was contributed between January 1 and April 18, 2017. Also make sure that you are not including the $4,500 when you tell TurboTax your year-end balance in traditional IRAs (which should be zero if you expect your entire $2,000 of basis to be applied to your Roth conversion).
