1. Did you indicate in the 1099-R interview that this was a military pension, in the screens after you enter the 1099-R?
2. In the Missouri interview, did you see the screens starting with "Missouri Pension and Retirement Adjustment"? The screens that follow should show you the calculations.
A brief glance suggests that your Social Security is netted against your military pension. Then look at Form MO-A, Part 3, Sections A, D, and E. If Section E is zero or blank, then your military pension exemption got reduced to zero.
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