If you entered the amount that was withheld in box 4 then it was applied to your withholding for the year. Adding the 1099-R to your other income may have increased the amount that you owed to more than the amount that was withheld even though there was extra withholding on the 1099-R.
In addition if the code in box 7 of your 1099-R is '1' then there is not just regular income tax assessed on the withdrawal there is an additional 10% penalty for taking it out early. This may be the number that you are seeing on your tax return.
@jrobwebster
**Say "Thanks" by clicking the thumb icon in a post
**Mark the post that answers your question by clicking on "Mark as Best Answer"
