Whether they show up as taxable on 1040 line 4b or 5b it won't change the tax on your return. But if they are on the wrong line the IRS might miss them and say you didn't report them and send you a bill. Is that what happened? Then you just need to tell them the income is on the other line.
On the 1099R the little IRA box is between boxes 7&8. That determines which line it goes to.
If you edit or review a 1099R it does not keep your answers from before but resets them to the defaults. Then you have to go through and answer them all again. So be sure to go all the way to the end of the 1099R section. They are right unless you go back.
