Retirement tax questions

The first time I ran it, the 1099R was like it was supplied to me, and no errors - but not untaxed.  That means I am paying tax again on the money I already paid tax on. The distribution was equal to all of the after tax amount I contributed.  Since the burden of proof for taxability is on the taxpayer, I thought the program should be able to handle it. But it appears not to be the case for this situation. I thank you again for your feedback.  I will further research the laws regarding the taxability of after tax contributions being distributed in one lump sum and how to present them in a return.