When you efile a copy of the 1099R is not sent. you only attach a copy if you mail your return.
Is the amount in box 1 on line 4a and the taxable amount on line 4b (or 5a & 5b)? And the withholding on line 25b? If it's there it was included. Then the IRS has a difference reason for wanting to see a copy of your 1099R. Maybe they didn't get the copy from the issuer or it doesn't match what the payer sent in.
