Where do you see it being taxable income? On 1040 line 4d?
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 your return and make sure it's right.
For 1099R check the actual 1040 line 4b or 4d for any taxable amount. If it was a rollover it should say ROLLOVER by the "b or d" line.
What code is on the 1099R box 7? If it's a G that is a direct rollover and not taxable. Did they take any withholding out of it in box 4?
