Is the box on your 1099-R for "Taxable amount not determined box is checked" checked? Then this is OK if a bit odd.
In the rest of the 1099-R interview, there will be a series of questions, the point of which is to determine how much of your pension income is taxable.
If you had made after-tax contributions to your pension plan while you were employed, then when these dollars are returned to you, you do not pay tax on them. However, these dollars - called your basis - are spread out over many years, and the point of the questions is to figure out how much is your basis, so how much your taxable income should be reduced.
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