The amounts from Box 1 on the 1099R are only flowing to the 1040 box 4a if it does NOT have the IRA box checked. The taxable portion, 1040 line 4b, is correct and includes the amounts from the 1099R box 2a regardless of if it is an IRA or a pension. But, this seems like box 4a should have ALL of the IRA and pension amounts listed so that the IRS can match it. In addition, it makes it hard to do a review when the gross distribution of the IRA is not listed anywhere on the tax return.