They don't match them up form by form, box to box. They are looking at totals. As long as you report all of your income on your return, you have nothing to be concerned about.
The only place to enter an amount for Box 6 is in the personal income section. If entered there, the taxable income goes on your return in the Other Income section. All of the farm expenses related to the income will still be deducted on your Schedule F. So, you are not losing out on any deductions by reporting the income in Box 6 in the personal section. The box 7 income can be reported in the Farm Income section. But the box 6 government income is reported with your personal income. You can enter the income from Box 6 using Forms Mode as described above - the tax will work out the same, but the descriptions as you see, won't match up perfectly.
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