What code is in box 7? After you enter the 1099R keep going. It should ask you what you did with the money. Say you moved it to another account even if you put it back into the same account. Were there any taxes withheld in box 4?
If you are looking at a summary screen or review screen those show the full amount as income and lump a lot of stuff together. You need to check the actual 1040 form and make sure it's right.
