Typically when the military W2 is not handled properly it is due to a missing selection after entering the form W2 information. Edit the form W2 in the federal "Wages & Income" section and after you verify the W2 form information you will arrive at a page asking about "Uncommon Situations". In that list there is an item for "Active Military Duty". Be sure to select that item and continue.
This should allow the correct handling of the military W2.