Military Pay comes from inputting the W-2 form in the Wages and Other Income section of the federal interview.
The screen immediately following the W-2 entry has a list of special issues which might have an effect on that W-2. Right at the top is a check box for this W-2 is for active duty military wages. If you check that box in the federal interview, the correct questions will be triggered in the Missouri interview so that military pay adjustment can be made.
Go back to the federal interview, Wages and Other Income, W-2s and click on Edit on the W-2 involved. Continue to the interview screen with the long list of check boxes. Click on the military check box and then go to state interview and go over MO again. You should see different screens and be able to get the correct adjustment for military wages.