After you file

@slc22 If you entered the Form 1099-R is the correct location in TurboTax, that information is included with your e-filed tax return.  Just like if you entered a W-2, that information is included with the e-filed tax return.

What exactly is the IRS complaining about in the letter you received?

 

I have been E-filing a Form 1099-R for the last twenty years with TurboTax, no IRS issues whatsoever.

 

To enter, edit or delete a form 1099-R -

Click on Federal Taxes (Personal using Home and Business)
Click on Wages and Income (Personal Income using Home and Business)
Click on I'll choose what I work on (if shown)
Scroll down to Retirement Plans and Social Security
On IRA, 401(k), Pension Plan Withdrawals (1099-R), click the start or update button