Second, check the Box 7 distribution code on the 1099-R screen to make sure you selected the correct distribution code. Generally, the code will be a 1 if its an early retirement distribution subject to the 10% penalty, or it will be a 7 if it is a normal retirement distribution.
Third, make sure you didn't select to treat the distribution as a rollover. On the screen right after the 1099-R screen, the Distribution Rollover screen, there is a checkbox that if marked, will treat the entire 1099-R distribution as being a rollover and not taxed. There is also an amount box on that screen where you can specify part of the distribution as a rollover. Make sure those aren't used if the 1099-R wasn't a rollover distribution.