The withholding in box 4 should be included in the amount on 1040 line 64 with all the withholding from your W2s etc. Doesn't line 64 have it added in? Did you enter the 1099R right?
I'm sure you already know this but just to explain it a little more:
You didn't actually pay the tax or 10% penalty (you pay a 10% early withdrawal penalty if you are under 59 ½). You had taxes withheld like from your paycheck. You still have to enter the whole amount (before taxes were withheld) with your other income to figure out the total tax (and it may put you into a higher tax bracket) and then the withholding is subtracted from the total tax to figure your refund or tax due. The withholding will show up on 1040 line 64 (2013 line 62) or 1040A line 36. The 10% penalty is on 1040 line 59 (2013 line 58).
So when you add all your income for year you didn't have enough withholding taken out of the 1099Rs to cover the total tax. You owe more than they sent in for taxes. That's very common to owe more because the withdrawals increase your income and put you into a higher tax bracket.
And by increasing your income it would have changed other items on your return like make more of your SS taxable or changed the limits on your Medical deductions or employee job expenses and changed any credits you qualified for.
Ps…..you can lose up to 50% of your withdrawal to federal and state taxes and penalties.
