The amount from box 2a on the Form 1099-R should have flowed to the Form 1040 Line 4b as taxable income and the amount of federal taxes withheld in box 4 should have flowed to the Form 1040 Line 25b as a tax payment. Did you indicate after entering the Form 1099-R that you rolled over the distribution to another tax deferred account or back to the same account? If so, this would made the distribution as not taxable.
